With more study, the technique could lead to new precision medicine pathology diagnostics and clinical laboratory tests
Researchers at Yale University have devised a new pathology tool that utilizes barcode technology to map the spatial relationships of ribonucleic acid (RNA) and proteins. This will be of interest to histopathologists who are responsible for examining clinical laboratory tissue samples and helping physicians diagnose disease.
Called Patho-DBiT (pathology-compatible deterministic barcoding in tissue), the Yale scientists claim their new tool can completely examine RNA and possibly aid in the diagnoses and treatment of cancer.
The technology, according to a Yale news release, “is unique in that it has microfluidic devices that deliver barcodes into the tissue from two directions creating a unique 2D ‘mosaic’ of pixels, providing spatial information that could be used to inform the creation of patient-specific targeted therapies.”
“It’s the first time we can directly ‘see’ all kinds of RNA species, where they are and what they do, in clinical tissue samples,” said Rong Fan, PhD, Harold Hodgkinson professor of biomedical engineering and pathology at Yale and senior author of the study.
“I think it’s going to completely transform how we study the biology of humans in the future,” said Rong Fan, PhD (above), Harold Hodgkinson professor of biomedical engineering and pathology at Yale and senior author of the study, in a Yale news release. The discovery could lead to new clinical laboratory screening tests and diagnostics for cancer. (Photo copyright: Yale University.)
More Precise Cancer Diagnoses
“As a physician who has been diagnosing cancer, I was surprised by how much more I can see using this pathology tool,” said Mina Xu, MD, professor of pathology at Yale School of Medicine and one of the authors of the study. “I think this deep molecular dive is going to advance our understanding of tumor biology exponentially. I really look forward to delivering more precise and actionable diagnoses.”
According to the Yale study, the Patho-DBiT tool has many beneficial capabilities. They include:
Dissecting spatiotemporal dynamics of lymphomagenesis at the single-cell level.
FFPE tissue involves the fixation of tissues by utilizing formalin and embedding tissue samples in paraffin wax. This method allows for the long-term preservation of tissue morphology and cellular details and is commonly used in histopathology.
In the past, the RNA within FFPE samples have been susceptible to fragmentation during the paraffin-embedding process and degradation issues. These samples may also experience chemical modifications which could result in resistance to the enzymatic reactions necessary for proper sequencing.
“There are millions of these tissues that have been archived for so many years, but up until now, we didn’t have effective tools to investigate them at spatial level,” said the study’s first author Zhiliang Bai, PhD, a postdoctoral associate in Rong Fan’s lab at Yale. “RNA molecules in these tissues we’re looking at are highly fragmented and traditional methods can’t capture all the important information about them. It’s why we’re very excited about Patho-DBiT.”
Targeted Therapies
The team is encouraged by their research and the future potential for Patho-DBiT. They believe the technology may be useful in creating targeted therapies and helping understand the metamorphosis of low-grade tumors to more aggressive ones. They conceive their tool may assist in developing ways to prevent the progression of cancers.
“It is very exciting that Patho-DBiT-seq is also capable of generating spatial maps of noncoding RNA expression,” said Jun Lu, PhD, associate professor of genetics at Yale and another of the study’s authors. “Noncoding RNAs are often in regions of our genomes that were previously thought of as junk DNA, but now they are recognized as treasured players in biology and diseases such as cancer.”
The research included faculty members from several departments at Yale and was supported by the National Institutes of Health (NIH). The technology is now licensed to biotechnology company AtlasXomics of New Haven, Ct., for further development.
More research and studies are needed to validate the findings of this research, but the Patho-DBiT tool could prove to be useful for the preservation of tissue samples and become essential in the diagnoses and treatment of cancers.
Further research could eventually lead to clinical laboratory biomarkers and screening tests to identify infants whose gut bacteria may predispose them to neurodevelopment disorders later in life
Microbiologists and clinical laboratory scientists working with gut bacteria will be intrigued to learn that a study conducted by scientists from Linköping University in Sweden and the Department of Microbiology and Cell Science at the University of Florida (UFL) recently found that gut microbiota (aka, gut flora) in infancy can be correlated with developing a neurodevelopmental disorder (ND) later in life.
The researchers analyzed patient records from the 20-year All Babies in Southeast Sweden (ABIS) prospective cohort study into the etiology of obesity, diabetes, and other diseases. They found that “disturbances” in the microbiomes of children during the first years of life could be linked to later ND diagnoses, according to Neuroscience News.
“We’ve found associations with some factors that affect gut bacteria, such as antibiotic treatment during the child’s first year, which is linked to an increased risk of these diseases,” stated pediatrician Johnny Ludvigsson, MD, PhD, Senior Professor, Department of Biomedical and Clinical Sciences at Linköping University, who co-led the study, in a Linköping University news release.
“Analyzing over 16,000 children from the ABIS study, researchers identified significant biomarkers in cord blood and stool samples that correlate with future diagnoses of these disorders,” Neuroscience News reported.
This study adds evidence to the growing theory that every individual’s microbiome has much to do with his/her state of health and specific health conditions.
“We can see in the study that there are clear differences in the intestinal flora already during the first year of life between those who develop autism or ADHD and those who don’t,” said pediatrician and study co-author Johnny Ludvigsson, MD, PhD (above), Senior Professor, Department of Biomedical and Clinical Sciences at Linköping University, in a news release. Clinical laboratory scientists and microbiologists who work with gut microbiota will find these observations intriguing. (Photo copyright: Linköping University.)
Analysis of the ABIS Study
To conduct their study, the researchers analyzed the health records of 16,440 children born between 1997 and 1999 who participated in the ABIS study. The subjects were a close representation of the general Swedish population and were followed from birth into their twenties.
Research showed that 1,197 of the 16,440 children (7.28%) had been diagnosed with either autism, ADHD, communication disorders, or an intellectual disability.
The researchers also surveyed the ABIS study participants concerning their lifestyles and environmental factors during childhood. They analyzed substances found in the umbilical cord blood and stool bacteria collected at age one in some of the study participants. Cord blood remains in the placenta and umbilical cord after birth and is rich in stem cells.
“The remarkable aspect of the work is that these biomarkers are found at birth in cord blood or in the child’s stool at one year of age over a decade prior to the diagnosis,” said Eric Triplett, PhD, Professor and Chair of the Department of Microbiology and Cell Science at UFL and a co-leader of the study, in the Linköping University news release.
The investigation found that children who had numerous ear infections during the first year of life were more prone to receiving a diagnosis of a neurodevelopmental disorder later in life. The scientists surmised that it was not the infections that caused the issues. Rather, it was that repeated antibiotic treatments had disturbed the balance of healthy gut bacteria.
“We’re not trying to say that antibiotics are necessarily a bad thing,” stated Angelica Ahrens, PhD, Assistant Research Scientist in the Triplett Research Group at the University of Florida and first author of the study, in a UFL blog. “But perhaps overuse can be detrimental to the microbiome, and for some children, for whatever reason, their microbiome might not recover as readily.”
Deficits in Important Bacteria
The researchers discovered that the presence of Citrobacter bacteria increased the risk of a future ND diagnosis. According to ScienceDirect, “organisms of the genus Citrobacter are gram-negative bacilli that are occasional inhabitants of the gastrointestinal tract and are responsible for disease in neonates [newborns that are four weeks or younger] and debilitated or immunocompromised patients.”
They also discovered that the absence of Coprococcus bacteria increased the risk of getting an ND as well. One of the main producers of butyrate, Coprococcus is known to support gut barrier function, suppress harmful bacteria, and contain anti-inflammatory properties.
“Coprococcus and Akkermansia muciniphila have potential protective effects,” said Ahrens in the Linköping University news release. “These bacteria were correlated with important substances in the stool, such as vitamin B and precursors to neurotransmitters which play vital roles orchestrating signaling in the brain. Overall, we saw deficits in these bacteria in children who later received a developmental neurological diagnosis.”
Environmental/Behavioral Findings of the ABIS Study
Through the analysis of toxins present in study participants’ cord blood, the researchers confirmed that risk of developing an ND increases when babies are exposed to parents who smoke. The scientists also found that breastfeeding offers a protective effect against NDs.
More research is needed to determine whether gut flora in infants can have an effect on developing NDs later in life, and it is not yet known if similar findings will be detected in other populations. Nevertheless, the findings that many biomarkers for NDs can be observed in infancy may enable scientists to create clinical laboratory screening protocols, preventative measures, and innovative treatments for neurodevelopmental disorders.
Further research and studies linking certain microbiome factors to specific health conditions will create opportunities for microbiologists and clinical laboratories as well, to perform diagnostic testing that identifies if a patient—in this case a newborn or infant—has a microbiome that will lead to immediate or later neurological health conditions.
Studies could lead to new prognostic biomarkers and clinical laboratory diagnostics for cancer
Might fungi be involved in human cancers? Two separately published studies have found fungal DNA in various cancers in the human body. However, the researchers are unclear on how the fungi got into the cancer cells and if it is affecting the cancers’ pathology. Nevertheless, these discoveries could lead to utilizing tumor-associated fungal DNA as clinical laboratory diagnostics or prognostic biomarkers in the fight against cancer.
“The finding that fungi are commonly present in human tumors should drive us to better explore their potential effects and re-examine almost everything we know about cancer through a ‘microbiome lens,’” said Ravid Straussman, MD, PhD (above), a principal investigator at Weizmann Institute of Science and one of the authors of the study in a UCSD press release. These findings could lead to new clinical laboratory diagnostics and prognostic biomarkers. (Photo copyright: Weizmann Institute of Science.)
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Microbiome Key to Cancer Biology and Detection
To perform their research, the team examined 17,401 samples of patient tissues, blood, and plasma across 35 different types of cancers in four independent cohorts. They discovered fungal DNA and cells in low abundances in many human cancers.
“The existence of fungi in most human cancers is both a surprise and to be expected,” said biologist Rob Knight, PhD, founding Director of the Center for Microbiome Innovation and Professor of Pediatrics and Computer Science and Engineering at UC San Diego in a UCSD press release. “It is surprising because we don’t know how fungi could get into tumors throughout the body. But it is also expected because it fits the pattern of healthy microbiomes throughout the body, including the gut, mouth and skin, where bacteria and fungi interact as part of a complex community.”
The main highlights of this study include:
Fungi detected in the different cancer types were often intracellular.
Multiple fungal-bacterial-immune ecologies were detected across tumors.
Intratumoral fungi stratified clinical outcomes, including immunotherapy response.
Cell-free fungal DNA found in both healthy and cancer patients in early-stage disease.
Fungi found on the human body appear as either environmental fungi, such as yeasts and molds, and commensal fungi, which live either on or inside the body. Both are typically harmless to most healthy people and can provide some benefits, such as improving gut health, but they may also be a contributing factor in some disease.
The researchers found that there were notable parallels between specific fungi and certain factors, such as age, tumor subtypes, smoking status, immunotherapy responses, and survival measures.
“These findings validate the view that the microbiome in its entirety is a key piece of cancer biology and may present significant translational opportunities, not only in cancer detection, but also in other biotech applications related to drug development, cancer evolution, minimal residual disease, relapse, and companion diagnostics,” said Gregory Sepich-Poore, MD, PhD, one of the study’s authors and co-founder and chief analytics officer at biotechnology company Micronoma, in the UCSD press release.
New Clinical Laboratory Tests to Identify Fungal Species in Cancer
Researchers from Duke University and Cornell University uncovered compelling evidence of fungi in multiple cancer types and focused on a detected link between Candida and gastrointestinal cancers.
They found that “several Candida species were enriched in tumor samples and tumor-associated Candida DNA was predictive of decreased survival,” according to their paper.
Their analysis of multiple body sites revealed tumor-associated mycobiomes in fungal cells. The researchers found that fungal spores known as blastomyces were associated with tumor tissues in lung cancers, and that high rates of Candida were present in stomach and colon cancers.
The Duke/Cornell researchers hope their work can provide a framework to develop new tests that can distinguish fungal species in tumors and predict cancer progression and help medical professionals and patients chose the best treatment therapies.
“These findings open up a lot of exciting research directions, from the development of diagnostics and treatments to studies of the detailed biological mechanisms of fungal relationships to cancers,” said Iliyan Iliev, PhD, Associate Professor of Microbiology and Immunology in Medicine, Weill Cornell Medicine, and one of the authors of the study, in a Weill news release.
More research is needed to determine if fungal DNA plays a role in disease pathology or if its presence does not have any causal link.
“It’s plausible that some of these fungi are promoting tumor progression and metastasis, but even if they aren’t, they could be very valuable as prognostic indicators,” Iliev said.
The insights gleaned from these two studies will be of particular interest to microbiologists, clinical laboratory professionals, and anatomic pathologists. Additional research could answer questions about how and if fungi infect tumors and if such fungi is a factor that increases cancer risk and outcomes.
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.
Pole-to-pole sampling of marine life leads researchers to conclude the world’s oceans could hold the key to many scientific and biotechnological advancements
Virologists and microbiologists will be intrigued to learn that scientists at Ohio State University (OSU) have identified nearly 200,000 previously unknown viruses living deep in the oceans. The catalog of 195,728 viruses could serve as a “road map” to a better understanding of ecosystems within the world’s oceans and the role they play in maintaining the health of the planet.
Though the research was not specifically directed at developing useful insights for clinical care, it could one day lead to new diagnostic assays or therapies. For clinical laboratories and anatomic pathology groups, this study demonstrates how understanding and knowledge about viruses and other organisms continue to grow.
The researches published their findings in the journal Cell.
Viruses Are Tiny but Important
The OSU researchers led a 24-member team’s effort to expand
the catalog of ocean viruses and draw the first global map of viral diversity.
“Viruses tend to steal genes and do really interesting
things with them. So, someone who’s savvy in biotechnology can mine this data
set to find new enzymes that can help us in our everyday lives, whether that’s
cosmetic products or creating a new thermocycler or some sort of engineering
process,” Matthew
Sullivan, PhD, a microbiologist at OSU and one of the study’s authors, told
CNN.
“Viruses are these tiny things that you can’t even see, but because they’re present in such huge numbers, they really matter,” Matthew Sullivan, PhD, a microbiologist at Ohio State University and one of the study’s authors, said in a new release. “We’ve developed a distribution map that is foundational for anyone who wants to study how viruses manipulate the ecosystem. There were many things that surprised us about our findings.” These new discoveries could someday form the basis for new medical laboratory tests and therapeutic drugs. (Photo copyright: Ohio State University.)
According to the news release, “The samples were collected during the unprecedented three-year Tara Oceans Expedition, in which a team of more than 200 experts took to the sea to catalog and better understand the unseen inhabitants of the ocean, from tiny animals to viruses and bacteria.”
“What was really exciting was now being able to study these viruses at two important levels—the population level and by looking at genetic variation within each population, which tells us about evolution,” Ann Gregory, PhD, co-lead author of the study, said in an OSU news release. “We have expanded the number of known viral populations more than tenfold and this new map will help us understand the impact of ocean viruses on a global level,” she added.
A news release from Tara Ocean Foundation notes that prior ocean surveys had identified 16,000 viral species.
Massive Quest for Knowledge
The OSU scientists studied ocean life from varying ocean depths, stretching from pole to pole, using samples collected during the Tara Oceans expeditions, which took place from 2009-2013. The Tara Ocean Foundation has backed 11 scientific expeditions and collected more than 60,000 samples that have been the basis for more than 70 scientific publications.
The team of researchers split the viruses into five
ecological zones: all depths of the Arctic and Antarctic and three distinct
depths of the Temperate and Tropical regions, noted the OSU study.
By developing new methods to sequence viruses in planktonic
populations, the OSU research team, according to the Tara Ocean press release,
was able to understand genetic variations:
Between individuals within each population;
Between populations within each viral community;
and
Between communities across several environments
of the global oceans, as well as study the driving forces behind all these
variations.
In its news release, Tara Ocean Foundation pointed out one
surprise was the “cradle of viral diversity” found in the Arctic Ocean, which
had not been part of earlier studies of ocean life.
“This research has significant implications for
understanding how ocean micro-organisms affect the atmosphere,” Sullivan said
in the Cell Press news release, which goes on to note that, “The investigators
say that having a more complete picture of marine viral distribution and
abundance will help them to determine which viruses they should be focusing on
for further studies.”
“Previous ocean ecosystem models have commonly ignored
microbes, and rarely included viruses, but we now know they are a vital
component to include,” said Sullivan.
At this time, the OSU study offers little that clinical
laboratories can use other than a deeper awareness of how viruses impact our
world and environment. However, further study of the ocean depths may yield
surprises that also expand medical knowledge and lead to new therapies and
diagnostic tests.
