The UE study sheds light on the types of bacteria in
wastewater that goes down hospital pipes to sewage treatment plants. The study
also revealed that not all infectious agents are killed after passing through
waste treatment plants. Some bacteria with antimicrobial (or antibiotic)
resistance survive to enter local food sources.
The scientists concluded that the amount of AMR genes found
in hospital wastewater was linked to patients’ length-of-stays and consumption
of antimicrobial resistant bacteria while in the hospital.
In a paper the University of Edinburgh published on medRxiv, the researchers wrote: “There was a higher abundance of antimicrobial-resistance genes in the hospital wastewater samples when compared to Seafield community sewage works … Sewage treatment does not completely eradicate antimicrobial-resistance genes and thus antimicrobial-resistance genes can enter the food chain through water and the use of [processed] sewage sludge in agriculture. As hospital wastewater contains inpatient bodily waste, we hypothesized that it could be used as a representation of inpatient community carriage of antimicrobial resistance and as such may be a useful surveillance tool.”
Additionally, they wrote, “Using metagenomics to identify
the full range of AMR genes in hospital wastewater could represent a useful
surveillance tool to monitor hospital AMR gene outflow and guide environmental
policy on AMR.”
Antimicrobial stewardship programs are becoming increasingly critical to preventing the spread of AMR bacteria. “By having those programs, [there are] documented cases of decreased antibiotic resistance within organisms causing these infections,” Paul Fey, PhD, of the University of Nebraska Medical Center, told MedPage Today. “This is another indicator of how all hospitals need to implement stewardship programs to have a good handle on decreasing antibiotic use.” [Photo copyright: University of Nebraska.]
Don’t Waste the Wastewater
Antibiotic resistance occurs when bacteria change in response to medications to prevent and treat bacterial infections, according to a World Health Organization (WHO) fact sheet. The CDC estimates that more than 23,000 people die annually from two million antibiotic-resistance infections.
Wastewater, the UE scientists suggest, should not go to
waste. It could be leveraged to improve hospitals’ detection of patients with antimicrobial
resistance, as well as to boost environment antimicrobial-resistance polices.
They used metagenomics (the study of genetic material
relative to environmental samples) to compare the antimicrobial-resistance
genes in hospital wastewater against wastewater from community sewage
points.
The UE researchers:
First collected samples over a 24-hour period from various areas in a tertiary hospital;
They then obtained community sewage samples from various locations around Seafield, Scotland;
Antimicrobial-resistance genes increased with longer length of patient stays, which “likely reflects transmission amongst hospital inpatients,” researchers noted.
Fey suggests that further research into using sequencing
technology to monitor patients is warranted.
“I think that monitoring each patient and sequencing their
bowel flora is more likely where we’ll be able to see if there’s a significant
carriage of antibiotic-resistant organisms,” Fey told MedPage Today. “In
five years or so, sequencing could become so cheap that we could monitor every
patient like that.”
Fey was not involved in the University of Edinburgh
research.
Given the rate at which AMR bacteria spreads, finding antibiotic-resistance
genes in hospital wastewater may not be all that surprising. Still, the University
of Edinburgh study could lead to cost-effective ways to test the genes of
bacteria, which then could enable researchers to explore different sources of
infection and determine how bacteria move through the environment.
And, perhaps most important, the study suggests clinical
laboratories have many opportunities to help eliminate infections and slow
antibiotic resistance. Microbiologists can help move their organizations forward
too, along with infection control colleagues.
Metabolic panels of 14 blood-based biomarkers that can predict when a patient is likely to die may be coming to a medical laboratory near you
Clinical pathologists soon may be able to predict when patients will die, thanks to a recent study that reveals new insights into how the human body works. Researchers at the Max Planck Institute for Biology of Ageing in Germany and the Leiden University Medical Center (LUMC) in the Netherlands revealed a metabolic panel of biomarkers that can more accurately predict death within five to 10 years than standard measures.
The researchers’ original goal was to find blood-based
biomarkers that could show whether a person was vulnerable to death,
particularly if that vulnerability was related to modifiable lifestyle factors.
The researchers published their study, titled, “A Metabolic Profile of All-Cause Mortality Risk Identified in an Observational Study of 44,168 Individuals,” in the journal Nature Communications last August.
Metabolic Biomarkers More Accurate than Current Health
Measures
During their investigation, the researchers looked at 12
cohorts from previous studies and examined the results of 44,168 individuals
between the ages of 18 and 109. In the follow-up to the study, 5,512 of the
participants died.
In the introduction to their published study the researchers
wrote, “We first determine which metabolic biomarkers independently associate
with prospective mortality in all individuals. Subsequently, we test the
association of the biomarkers with mortality in different age strata.”
The researchers then used the 14 biomarkers they identified to
create a score that predicts mortality within five to 10 years.
The measures that most providers currently use to determine an elderly person’s overall health generally include blood pressure, heart rate, and functionality measures such as grip strength and gait. However, P. Eline Slagboom, PhD, LUMC Professor of Molecular Epidemiology and the study’s director, told The Scientist that those metrics are not always accurate methods for measuring health.
“For example, a somewhat higher weight, blood pressure, or
cholesterol level is not as bad for individuals over 80 years of age as
compared to younger individuals,” she said.
As it turned out, the traditional measures were
significantly less accurate than the score Slagboom and her team developed.
Traditional measures were accurate about 78% of the time, while the metabolic
panel was accurate about 83% of the time, reported The Scientist.
Additionally, the score based on metabolic biomarkers was accurate for people
of all ages, rather than only among the young.
“As researchers on aging, we are keen to determine the biological age. The calendar age just doesn’t say very much about the general state of health of elderly people: one 70-year old is healthy, while another may already be suffering from three diseases. We now have a set of biomarkers which may help to identify vulnerable elderly people,” said P. Eline Slagboom, PhD (above), LUMC Professor of Molecular Epidemiology and the study’s director, in a statement. (Photo copyright: Max Planck Institute for Biology of Ageing.)
Study Yields Strong but Surprising Results
Researchers have studied biomarkers as predictive tools for quite some time, with only narrow success. The positive results of the Max Planck Institute/LUMC study even surprised those who worked on it. “We were surprised that the association of our biomarker score with mortality was so strong, given that it is only based on 14 metabolic markers in the blood measured at a single point in the life of individuals,” the study’s lead author Joris Deelen, PhD, a postdoctoral researcher at the Max Planck Institute for Biology of Ageing, said in The Scientist.
But though the results of the study are intriguing, some
experts remain skeptical that a new biomarker for death has been found.
In reactions published by the Science Media Centre, an independent organization in the UK that promotes “the reporting of evidence-based science,” Kevin McConway, PhD, Emeritus Professor of Applied Statistics at The Open University wrote, “This is a solid and interesting piece of research. But it doesn’t go beyond investigating the plausibility of setting up a system for predicting risk of death, based on this type of data. It doesn’t claim to do more than that, and makes clear that there’s some way to go, in terms of research and analysis, until a risk prediction tool that’s useable in clinical work with patients might emerge.”
And in the same article, Amanda Heslegrave, PhD, a post-doctoral research associate and researcher at the UK Dementia Research Institute at the University College London wrote, “Whilst this study shows that this type of profiling can be useful, [the researchers] do point out importantly that it would need further work to develop a score at the individual level that would be useful in real life situations. We’d need to see: validation to ensure repeatability in different labs, production of reference samples to test this on an ongoing basis, work to make the individual score possible, validation in other cohorts and validation of all components of the panel. So, it’s an exciting step, but it’s not ready yet.”
Past Mortality Biomarker Studies
Other investigations into the use of biomarkers as a predictive tool have focused more narrowly on specific causes of death. For example, in 2008, the New England Journal of Medicine (NEJM) published a study titled, “Use of Multiple Biomarkers to Improve the Prediction of Death from Cardiovascular Causes.” The study concluded that using biomarkers and risk factors together “substantially improves the risk stratification for death from cardiovascular causes.”
Another study, from 2017, examined stress biomarkers, hospital readmission, and death. Published in the Journal of Hospital Medicine titled, “Association of Stress Biomarkers with 30-Day Unplanned Readmission and Death,” the researchers found that “stress biomarkers improved the performance of prediction models and therefore could help better identify high-risk patients.”
Other studies have examined the predictive possibilities of
biomarkers in:
Even with all of the research into biomarkers, scientists are still a long way from having a clinical tool to predict death. However, according to Leo Cheng, PhD, Associate Biophysicist, Pathology and Radiology at Massachusetts General Hospital, and Associate Professor of Radiology at Harvard Medical School, the Max Planck study is on the right path.
The Scientist states that though Cheng believes the
study doesn’t “prove anything,” he also notes that “using a score that combines
the information from all 14 biomarkers is ‘the correct thing [to do]’ to
provide a holistic look at metabolic pathways that may represent a person’s
health.”
So, it might be awhile before clinical laboratories will be
processing metabolic panels that return test results predicting a patient’s
mortality within 10-15 years. Nevertheless, how medical labs would be involved
in such testing is certainly something to think about.
Use of synthetic genetics to replicate an infectious disease agent is a scientific accomplishment that many microbiologists and clinical laboratory managers expected would happen
Microbiologists and infectious disease doctors are quite familiar with Escherichia coli (E. coli). The bacterium has caused much human sickness and even death around the globe, and its antibiotic resistant strains are becoming increasingly difficult to eradicate.
Now, scientists in England have created a synthetic “recoded” version of E. coli bacteria that is being used in a positive way—to fight disease. Their discovery is being heralded as an important breakthrough in the quest to custom-alter DNA to create synthetic forms of life that one day could be designed to fight specific infections, create new drugs, or produce tools to diagnose or treat disease.
Scientists worldwide working in the field of synthetic genomics are looking for ways to modify genomes in order to produce new weapons against infection and disease. This research could eventually produce methods for doctors—after diagnosing a patient’s specific strain of bacteria—to then use custom-altered DNA as an effective weapon against that patient’s specific bacterial infection.
This latest milestone is the result of a five-year quest by researchers at the Medical Research Council Laboratory of Molecular Biology (MRC-LMB) in Cambridge, England, to create a man-made version of the intestinal bacteria by redesigning its four-million-base-pair genetic code.
The MRC-LMB lab’s success marks the first time a living
organism has been created with a compressed genetic code.
The researchers published their findings in the journal Nature.
“This is a landmark in the emerging field of synthetic
genomics and finally applies the technology to the laboratory’s workhorse
bacterium,” they wrote. “Synthetic genomics offers a new way of life, while at
the same time moving synthetic biology towards a future in which genomes can be
written to design.”
All known forms of life on Earth contain 64 codons—a specific sequence of three consecutive nucleotides that corresponds with a specific amino acid or stop signal during protein synthesis. Jason Chin, PhD, Program Lead at MRC-LMB, said biologists long have questioned why there are 20 amino acids encoded by 64 codons.
“Is there any function to having more than one codon to encode each amino acid?” Chin asked during an interview with the Cambridge Independent. “What would happen if you made an organism that used a reduced set of codons?”
The MRC-LMB research team took an important step toward
answering that question. Their synthetic E. coli strain, dubbed Syn61,
was recoded through “genome-wide substitution of target codons by defined
synonyms.” To do so, researchers mastered a new piece-by-piece technique that
enabled them to recode 18,214 codons to create an organism with a 61-codon
genome that functions without a previously essential transfer RNA.
“Our synthetic genome implements a defined recoding and refactoring scheme–with simple corrections at just seven positions–to replace every known occurrence of two sense codons and a stop codon in the genome,” lead author Julius Fredens, PhD, a post-doctoral research associate at MRC, and colleagues, wrote in their paper.
Science Alert reports that the laboratory-created version of E. coli (above) “isn’t quite a dead ringer for its ancestor. The cells are a touch longer, and they reproduce 1.6 times slower. But the edited E. coli seems healthy and produces the same range and quantity of proteins as the non-edited versions.” (Photo copyright: Jason Chin/STAT.)
Joshua Atkinson, PhD, a postdoctoral research associate at Rice University in Houston, labeled the breakthrough a “tour de force” in the field of synthetic genomics. “This achievement sets a new world record in synthetic genomics by yielding a genome that is four times larger than the pioneering synthesis of the one-million-base-pair Mycoplasma mycoides genome,” he stated in Synthetic Biology.
“Synthetic genomics is enabling the simplification of
recoded organisms; the previous study minimized the total number of genes and
this new study simplified the way those genes are encoded.”
Manmade Bacteria That are Immune to Infections
Researchers from the J.
Craig Venter Institute in Rockville, Maryland, created the first synthetic
genome in 2010. According to an article in Nature,
the Venter Institute successfully synthesized the Mycoplasma mycoides genome
and used it “reboot” a cell from a different species of bacterium.
The MRC-LMB team’s success may prove more significant.
“This new synthetic E. coli should not be able to decode DNA from any other organism and therefore it should not be possible to infect it with a virus,” the MRC-LMB stated in a news release heralding the lab’s breakthrough. “With E. coli already being an important workhorse of biotechnology and biological research, this study is the first time any commonly used model organism has had its genome designed and fully synthesized and this synthetic version could become an important resource for future development of new types of molecules.”
Because the MRC-LMB team was able to remove transfer RNA and
release factors that decode three codons from the E. coli bacteria,
their achievement may be the springboard to designing manmade bacteria that are
immune to infections or could be turned into new drugs.
“This may enable these codons to be cleanly reassigned and
facilitate the incorporation of multiple non-canonical amino acids. This
greatly expands the scope of using non-canonical amino acids as unique tools
for biological research,” the MRC-LMB news release added.
Though synthetic genomics impact on clinical laboratory diagnostics is yet to be known, medical laboratory leaders should be mindful of the potential for rapid innovation in this field as proof-of-concept laboratory innovations are translated into real-world applications.
The proof-of-concept experiment showed data can be encoded in DNA and retrieved using automated systems, a development that may have positive significance for clinical laboratories
It may seem far-fetched, but computer scientists and research groups have worked for years to discover if it is possible to store data on Deoxyribonucleic acid (DNA). Now, Microsoft Research (MR) and the University of Washington (UW) have achieved just that, and the implications of their success could be far-reaching.
Clinical pathologists are increasingly performing genetic DNA sequencing in their medical laboratories to identify biomarkers for disease, help clinicians understand their patients’ risk for a specific disease, and track the progression of a disease. The ability to store data in DNA would take that to another level and could have an impact on diagnostic pathology. Pathologist familiar with DNA sequencing may find a whole new area of medical service open to them.
The MR/UW researchers recently demonstrated a fully automated system that encoded data into DNA and then recovered the information as digital data. “In a simple proof-of-concept test, the team successfully encoded the word ‘hello’ in snippets of fabricated DNA and converted it back to digital data using a fully automated end-to-end system,” Microsoft stated in a news release.
DNA’s Potential Storage Capacity and Why We Need It
Thus far, the challenge of using DNA for data storage has
been that there wasn’t a way to easily code and retrieve the information. That,
however, seems to be changing quite rapidly. Several major companies have
invested heavily in research, with consumer offerings expected soon.
At Microsoft Research, ‘consumer interest’ in genetic testing has driven the research into using DNA for data storage. “As People get better access to their own DNA, why not also give them the ability to read any kind of data written in DNA?” asked Doug Carmean, an Architect at Microsoft, during an interview with Wired.
Scientists are interested in using DNA for data storage because
humanity is creating more data than ever before, and the pace is accelerating.
Currently, most of that data is stored on tape, which is inexpensive, but has
drawbacks. Tape degrades and has to be replaced every 10 years or so. But DNA,
on the other hand, lasts for thousands of years!
“DNA won’t degrade over time like cassette tapes and CDs, and it won’t become obsolete,” Yaniv Erlich, PhD, Chief Science Officer at MyHeritage, an online genealogy platform located in Israel, and Associate Professor, Columbia University, told Science Mag.
Tape also takes up an enormous amount of physical space compared to DNA. One single gram of DNA can hold 215 petabytes (roughly one zettabyte) of data. Wired puts the storage capacity of DNA into perspective: “Imagine formatting every movie ever made into DNA; it would be smaller than the size of a sugar cube. And it would last for 10,000 years.”
Researchers at the University of Washington claim, “All the movies, images, emails and other digital data from more than 600 basic smartphones (10,000 gigabytes) can be stored in the faint pink smear of DNA at the end of this test tube.” (Photo and caption copyright: Tara Brown/University of Washington.)
Victor Zhirnov, Chief Scientist at Semiconductor Research Corporation says the worries over storage space aren’t simply theoretical. “Today’s technology is already close to the physical limits of scaling,” he told Wired, which stated, “Five years ago humans had produced 4.4 zettabytes of data; that’s set to explode to 160 zettabytes (each year!) by 2025. Current infrastructure can handle only a fraction of the coming data deluge, which is expected to consume all the world’s microchip-grade silicon by 2040.”
MIT Technology Review agrees, stating, “Humanity is creating information at an unprecedented rate—some 16 zettabytes every year. And this rate is increasing. Last year, the research group IDC calculated that we’ll be producing over 160 zettabytes every year by 2025.”
Heavy Investment by Major Players
The whole concept may seem like something out of a science
fiction story, but the fact that businesses are investing real dollars into it
is evidence that DNA for data storage will likely be a reality in the near
future. Currently, there are a couple of barriers, but work is commencing to
overcome them.
First, the cost of synthesizing DNA in a medical laboratory
for the specific purpose of data storage must be cheaper for the solution to
become viable. Second, the sequencing process to read the information must also
become less expensive. And third is the problem of how to extract the data
stored in the DNA.
In a paper published in ASPLOS ‘16, the MR/UW scientists wrote: “Today, neither the performance nor the cost of DNA synthesis and sequencing is viable for data storage purposes. However, they have historically seen exponential improvements. Their cost reductions and throughput improvements have been compared to Moore’s Law in Carlson’s Curves … Important biotechnology applications such as genomics and the development of smart drugs are expected to continue driving these improvements, eventually making data storage a viable application.”
Automation appears to be the final piece of the puzzle. Currently,
too much human labor is necessary for DNA to be used efficiently as data
storage.
“Our ultimate goal is to put a system into production that, to the end user, looks very much like any other cloud storage service—bits are sent to a datacenter and stored there and then they just appear when the customer wants them,” said Microsoft principal researcher Karin Strauss (above), in the Microsoft news release. “To do that, we needed to prove that this is practical from an automation perspective.” Click here to watch a Microsoft Research video on the DNA storage process. (Photo copyright: Microsoft Research/YouTube.)
It may take some time before DNA becomes a viable medium for
data storage. However, savvy pathology laboratory managers should be aware of,
and possibly prepared for, this coming opportunity.
While it’s unlikely the average consumer will see much
difference in how they save and retrieve data, medical laboratories with the
ability to sequence DNA may find themselves very much in demand because of
their expertise in sequencing DNA and interpreting gene sequences.
CDC estimates that 92% of cancers caused by HPV could be eliminated in the US if HPV vaccination recommendations in this country are followed
Medical
laboratories in the United States once processed as many as 55-million Pap tests each year. However,
the need for cervical cancer screening tests is diminishing. That’s primarily because
the human
papilloma virus (HPV) vaccination effectively eliminates new cases of
cervical cancer. At least, that’s what’s happening in Australia.
When it was introduced in 2007, Australia’s nationwide
publicly-funded HPV
vaccination program only included girls, but was extended to boys in 2013.
Today, it is being credited with helping slash the country’s cervical cancer
rates.
Research published in The
Lancet Public Health (Lancet) predicts cervical cancer could be
eliminated in Australia by 2028 if current vaccination rates and screening
programs continue. Cervical cancer would be classified as effectively
eliminated once there are four or fewer new cases per 100,000 women each year.
These developments will be of interests to pathologists and cytotechnologists in
the United States.
“From the beginning, I think the [Australian] government
successfully positioned the advent of HPV vaccination as a wonderful package
that had a beneficial effect for the population,” Karen
Canfell, PhD, Director, Cancer Research Division at Cancer Council New
South Wales, Australia, and Adjunct Professor, University
of Sydney, told the Texas
Tribune. “It was celebrated for that reason, and it was a great public
health success.”
In addition to high vaccination rates, the Lancet
study notes that last year Australia transitioned from cytology-based cervical screening
every two years for women aged 18 to 69 years, to primary HPV testing every
five years for women aged 25 to 69 and exit testing for women aged 70 to 74
years.
“Large-scale clinical trials and detailed modelling suggest
that primary HPV screening is more effective at detecting cervical
abnormalities and preventing cervical cancer than screening with cytology at
shorter intervals,” the Lancet study states.
The incidence of cervical cancer in Australia now stands at
seven cases per 100,000. That’s about half the global average. The country is
on pace to see cervical cancer officially considered a “rare” cancer by 2020,
when rates are projected to drop to fewer than six new cases per 100,000 women.
US Cervical Cancer Rates
In Texas, meanwhile, the state’s failure to embrace HPV
vaccination is being blamed for slowing potential improvements in cervical
cancer rates. In 2007, Texas lawmakers rejected legislation that would have
mandated girls entering sixth grade be vaccinated for HPV. The Texas Tribune
reports that, in the decade that followed, vaccination rates remained stagnant
with only about 40% of Texans between 13 and 17 years old having been vaccinated
for HPV by 2017.
Though Texas has a similar size population as Australia, the
state’s low vaccination rates have meant cervical cancer rates have shown
little improvement. Statistics compiled by the federal Centers for Disease Control
and Prevention (CDC) show that Texas’ age-adjusted rate of new cervical
cancer cases sits at 9.2 per 100,000 women—unchanged since 2006.
Texas has the fifth highest rate of cervical cancer in the
nation, according to the CDC.
Texas State Rep. Jessica Farrar, a Democrat from Houston, maintains Texas should have followed the example of Australia, which in 2007 began a publicly funded HPV vaccination program that has the country on the verge of eliminating cervical cancer by 2028. Texas rejected mandatory HPV vaccinations and now has one of the highest cervical cancer rates in the US. “This is a preventable disease, and we should and can be doing more,” she told the Texas Tribune. “Here we are 12 years later, and look where we could’ve been, but because of certain beliefs, we’re suffering from cancers that could have been avoided.” (Photo copyright: The Texas Tribune.)
Lois Ramondetta,
MD, Professor of Gynecologic Oncology at MD Anderson Cancer Center in Houston,
told the Texas Tribune the state ignored an opportunity that Australia
seized. “[Australia] embraced the vaccine at that time, and our fear kind of
began around then,” Ramondetta said. “Really, vaccination in general has just
gone down the tube since then.”
CDC Study Pushes HPV Vaccination Recommendations in US
Texas is not the only state failing to capitalize on the HPV
vaccine’s cancer-curing promise. The CDC recently stated in a news
release announcing a recent study that 92% of cancers caused by HPV could
be eliminated if HPV vaccine recommendations were followed. CDC published the
study in its Morbidity
and Mortality Weekly Report.
HPV is a common virus that is linked to not only cervical
cancer but also cancers of the penis, head, and neck, as well as conditions
like genital warts. Though the CDC recommends children get the two-dose vaccine
at ages 11-12, the study findings indicate that only 51% of teens ages 11 to 17
have received the recommended doses of HPV vaccine, a 2% increase from 2017 to
2018.
“A future without HPV cancers is within reach, but urgent
action is needed to improve vaccine coverage rates,” Brett
Giroir, MD, Assistant Secretary for Health, US Department of Health and
Human Services (HHS), stated in the CDC news release. “Increasing HPV
vaccination overage to 80% has been and will continue to be a priority
initiative for HHS, and we will continue to work with our governmental and
private sector partners to make this a reality.”
Can Australia Eliminate Cervical Cancer?
University of Queensland Professor Ian Frazer, MD, who
co-authored the Lancet Public Health study, believes Australia is on the
verge not only of eliminating cervical cancer, but also eradicating the HPV
virus itself.
“Because this human papillomavirus only infects humans, and
the vaccine program prevents the spread of the virus, eventually we’ll get rid
of it, like we did with smallpox,” Frazer told The
Age.
“It’s not going to happen in my lifetime,” he added. “But it
could happen in the lifetime of my kids if they go about it the right way.”
If Australia’s combination of high HPV vaccination rates and
new HPV screening program succeeds in effectively eliminating cervical cancer,
clinical laboratories in this country should expect stepped-up efforts to
increase HPV vaccination rates in the United States. A renewed focus on reducing—and
ultimately eliminating—cervical cancer, could lead to fewer or less-frequently
performed Pap tests as part of cervical cancer screening protocols.
Genetic data captured by this new technology could lead to a new understanding of how different types of cells exchange information and would be a boon to anatomic pathology research worldwide
What if it were possible to map the interior of cells and view their genetic sequences using chemicals instead of light? Might that spark an entirely new way of studying human physiology? That’s what researchers at the Massachusetts Institute of Technology (MIT) believe. They have developed a new approach to visualizing cells and tissues that could enable the development of entirely new anatomic pathology tests that target a broad range of cancers and diseases.
Scientists at MIT’s Broad Institute and McGovern Institute for Brain Research developed this new technique, which they call DNA Microscopy. They published their findings in Cell, titled, “DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction.”
Joshua Weinstein, PhD, a postdoctoral associate at the Broad Institute and first author of the study, said in a news release that DNA microscopy “is an entirely new way of visualizing cells that captures both spatial and genetic information simultaneously from a single specimen. It will allow us to see how genetically unique cells—those comprising the immune system, cancer, or the gut for instance—interact with one another and give rise to complex multicellular life.”
The news release goes on to state that the new technology “shows
how biomolecules such as DNA and RNA are organized in cells and tissues,
revealing spatial and molecular information that is not easily accessible
through other microscopy methods. DNA microscopy also does not require
specialized equipment, enabling large numbers of samples to be processed
simultaneously.”
The images above, taken from the MIT study, compares optical imaging of a cell population (left) with an inferred visualization of the same cell population based on the information provided by DNA microscopy (right). Scale bar = 100 μm (100 micrometers). This technology has the potential to be useful for anatomic pathologists at some future date. (Photo and caption copyrights: Joshua Weinstein, PhD, et al/Cell.)
New Way to Visualize Cells
The MIT researchers saw an opportunity for DNA microscopy to
find genomic-level cell information. They claim that DNA microscopy images
cells from the inside and enables the capture of more data than with
traditional light microscopy. Their new technique is a chemical-encoded
approach to mapping cells that derives critical genetic insights from the
organization of the DNA and RNA in cells and tissue.
And that type of genetic information could lead to new precision medicine treatments for chronic disease. New Atlas notes that “ Speeding the development of immunotherapy treatments by identifying the immune cells best suited to target a particular cancer cell is but one of the many potential application for DNA microscopy.”
In their published study, the scientists note that “Despite enormous progress in molecular profiling of cellular constituents, spatially mapping [cells] remains a disjointed and specialized machinery-intensive process, relying on either light microscopy or direct physical registration. Here, we demonstrate DNA microscopy, a distinct imaging modality for scalable, optics-free mapping of relative biomolecule positions.”
How DNA Microscopy Works
The New York Times (NYT) notes that the advantage of DNA microscopy is “that it combines spatial details with scientists’ growing interest in—and ability to measure—precise genomic sequences, much as Google Street View integrates restaurant names and reviews into outlines of city blocks.”
And Singularity Hub notes that “ DNA microscopy, uses only a pipette and some liquid reagents. Rather than monitoring photons, here the team relies on ‘bar codes’ that chemically tag onto biomolecules. Like cell phone towers, the tags amplify, broadcasting their signals outward. An algorithm can then piece together the captured location data and transform those GPS-like digits into rainbow-colored photos. The results are absolutely breathtaking. Cells shine like stars in a nebula, each pseudo-colored according to their genomic profiles.”
“We’ve used DNA in a way that’s mathematically similar to photons in light microscopy,” Weinstein said in the Broad Institute news release. “This allows us to visualize biology as cells see it and not as the human eye does.”
In their study, researchers used DNA microscopy to tag RNA
molecules and map locations of individual human cancer cells. Their method is
“surprisingly simple” New Atlas reported. Here’s how it’s done,
according to the MIT news release:
Small synthetic DNA tags (dubbed “barcodes” by the MIT team) are added to biological samples;
The “tags” latch onto molecules of genetic material in the cells;
The tags are then replicated through a chemical reaction;
The tags combine and create more unique DNA labels;
The scientists use a DNA sequencer to decode and reconstruct the biomolecules;
A computer algorithm decodes the data and converts it to images displaying the biomolecules’ positions within the cells.
The visualization above was created from data gathered by DNA microscopy, which peers inside individual cells. It demonstrates how DNA microscopy enables scientists to identify different cells (colored dots) within a sample—with no prior knowledge of what the sample looks like. (Photo and caption copyright: Joshua Weinstein, PhD, et al./Cell.)
“The first time I saw a DNA microscopy image, it blew me away,” said Aviv Regev, PhD, a biologist at the Broad Institute, a Howard Hughes Medical Institute (HHMI) Investigator, and co-author of the MIT study, in an HHMI news release. “It’s an entirely new category of microscopy. It’s not just a technique; it’s a way of doing things that we haven’t ever considered doing before.”
Precision Medicine Potential
“Every cell has a unique make-up of DNA letters or genotype. By capturing information directly from the molecules being studied, DNA microscopy opens up a new way of connecting genotype to phenotype,” said Feng Zhang, PhD, MIT Neuroscience Professor,
Core Institute Member of the Broad Institute, and
Investigator at the McGovern Institute for Brain Research at MIT, in the HHMI
news release.
In other words, DNA microscopy could someday have applications in precision medicine. The MIT researchers, according to Stat, plan to expand the technology further to include immune cells that target cancer.
The Broad Institute has applied for a patent on DNA
microscopy. Clinical laboratory and anatomic pathology group leaders seeking
novel resources for diagnosis and treatment of cancer may want to follow the MIT
scientists’ progress.
