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Experimental Low-Cost Blood Test Can Detect Multiple Cancers, Researchers Say

Test uses a new ultrasensitive immunoassay to detect a known clinical laboratory diagnostic protein biomarker for many common cancers

Researchers from Mass General Brigham, the Dana-Farber Cancer Institute, Harvard University’s Wyss Institute and other institutions around the world have reportedly developed a simple clinical laboratory blood test that can detect a common protein biomarker associated with multiple types of cancer, including colorectal, gastroesophageal, and ovarian cancers.

Best of all, the researchers say the test could provide an inexpensive means of early diagnosis. This assay could also be used to monitor how well patients respond to cancer therapy, according to a news release.

The test, which is still in experimental stages, detects the presence of LINE-1 ORF1p, a protein expressed in many common cancers, as well as high-risk precursors, while having “negligible expression in normal tissues,” the researchers wrote in a paper they published in Cancer Discovery titled, “Ultrasensitive Detection of Circulating LINE-1 ORF1p as a Specific Multicancer Biomarker.”

The protein had previously been identified as a promising biomarker and is readily detectable in tumor tissue, they wrote. However, it is found in extremely low concentrations in blood plasma and is “well below detection limits of conventional clinical laboratory methods,” they noted.

To overcome that obstacle, they employed an ultra-sensitive immunoassay known as a Simoa (Single-Molecule Array), an immunoassay platform for measuring fluid biomarkers.

“We were shocked by how well this test worked in detecting the biomarker’s expression across cancer types,” said lead study author gastroenterologist Martin Taylor, MD, PhD, Instructor in Pathology, Massachusetts General Hospital and Harvard Medical School, in the press release. “It’s created more questions for us to explore and sparked interest among collaborators across many institutions.”

Kathleen Burns, MD, PhD

“We’ve known since the 1980s that transposable elements were active in some cancers, and nearly 10 years ago we reported that ORF1p was a pervasive cancer biomarker, but, until now, we haven’t had the ability to detect it in blood tests,” said pathologist and study co-author Kathleen Burns, MD, PhD (above), Chair of the Department of Pathology at Dana-Farber Cancer Institute and a Professor of Pathology at Harvard Medical School, in a press release. “Having a technology capable of detecting ORF1p in blood opens so many possibilities for clinical applications.” Clinical laboratories may soon have a new blood test to detect multiple types of cancer. (Photo copyright: Dana-Farber Cancer Institute.)

Simoa’s Advantages

In their press release, the researchers described ORF1p as “a hallmark of many cancers, particularly p53-deficient epithelial cancers,” a category that includes lung, breast, prostate, uterine, pancreatic, and head and neck cancers in addition to the cancers noted above.

“Pervasive expression of ORF1p in carcinomas, and the lack of expression in normal tissues, makes ORF1p unlike other protein biomarkers which have normal expression levels,” Taylor said in the press release. “This unique biology makes it highly specific.”

Simoa was developed at the laboratory of study co-author David R. Walt, PhD, the Hansjörg Wyss Professor of Bioinspired Engineering at Harvard Medical School, and Professor of Pathology at Harvard Medical School and Brigham and Women’s Hospital.

The Simoa technology “enables 100- to 1,000-fold improvements in sensitivity over conventional enzyme-linked immunosorbent assay (ELISA) techniques, thus opening the window to measuring proteins at concentrations that have never been detected before in various biological fluids such as plasma or saliva,” according to the Walt Lab website.

Simoa assays take less than two hours to run and require less than $3 in consumables. They are “simple to perform, scalable, and have clinical-grade coefficients of variation,” the researchers wrote.

Study Results

Using the first generation of the ORF1p Simoa assay, the researchers tested blood samples of patients with a variety of cancers along with 406 individuals, regarded as healthy, who served as controls. The test proved to be most effective among patients with colorectal and ovarian cancer, finding detectable levels of ORF1p in 58% of former and 71% of the latter. Detectable levels were found in patients with advanced-stage as well as early-stage disease, the researchers wrote in Cancer Discovery.

Among the 406 healthy controls, the test found detectable levels of ORF1p in only five. However, the control with the highest detectable levels, regarded as healthy when donating blood, “was six months later found to have prostate cancer and 19 months later found to have lymphoma,” the researchers wrote.

They later reengineered the Simoa assay to increase its sensitivity, resulting in improved detection of the protein in blood samples from patients with colorectal, gastroesophageal, ovarian, uterine, and breast cancers.

The researchers also employed the test on samples from 19 patients with gastroesophageal cancer to gauge its utility for monitoring therapeutic response. Although this was a small sample, they found that among 13 patients who had responded to therapy, “circulating ORF1p dropped to undetectable levels at follow-up sampling.”

“More Work to Be Done”

The Simoa assay has limitations, the researchers acknowledged. It doesn’t identify the location of cancers, and it “isn’t successful in identifying all cancers and their subtypes,” the press release stated, adding that the test will likely be used in conjunction with other early-detection approaches. The researchers also said they want to gauge the test’s accuracy in larger cohorts.

“The test is very specific, but it doesn’t tell us enough information to be used in a vacuum,” Walt said in the news release. “It’s exciting to see the early success of this ultrasensitive assessment tool, but there is more work to be done.”

More studies will be needed to valid these findings. That this promising new multi-cancer immunoassay is based on a clinical laboratory blood sample means its less invasive and less painful for patients. It’s a good example of an assay that takes a proteomic approach looking for protein cancer biomarkers rather than the genetic approach looking for molecular DNA/RNA biomarkers of cancer.

—Stephen Beale

Related Information:

Ultrasensitive Blood Test Detects ‘Pan-Cancer’ Biomarker

New Blood Test Could Offer Earlier Detection of Common Deadly Cancers

Ultrasensitive Detection of Circulating LINE-1 ORF1p as a Specific Multicancer Biomarker

Noninvasive and Multicancer Biomarkers: The Promise of LINE-1 Retrotransposons

LINE-1-ORF1p Is a Promising Biomarker for Early Cancer Detection, But More Research Is Needed

‘Pan-Cancer’ Found in Highly Sensitive Blood Test

Cambridge Researchers in UK Develop ‘Unknome Database’ That Ranks Proteins by How Little is Known about Their Functions

Scientists believe useful new clinical laboratory assays could be developed by better understanding the huge number of ‘poorly researched’ genes and the proteins they build

Researchers have added a new “-ome” to the long list of -omes. The new -ome is the “unknome.” This is significant for clinical laboratory managers because it is part of an investigative effort to better understand the substantial number of genes, and the proteins they build, that have been understudied and of which little is known about their full function.

Scientists at the Medical Research Council Laboratory of Molecular Biology (MRC-LMB) in Cambridge, England, believe these genes are important. They have created a database of thousands of unknown—or “unknome” as they cleverly dubbed them—proteins and genes that have been “poorly understood” and which are “unjustifiably neglected,” according to a paper the scientist published in the journal PLOS Biology titled, “Functional Unknomics: Systematic Screening of Conserved Genes of Unknown Function.”

The Unknome Database includes “thousands of understudied proteins encoded by genes in the human genome, whose existence is known but whose functions are mostly not,” according to a news release.

The database, which is available to the public and which can be customized by the user, “ranks proteins based on how little is known about them,” the PLOS Biology paper notes.

It should be of interest to pathologists and clinical laboratory scientists. The fruit of this research may identify additional biomarkers useful in diagnosis and for guiding decisions on how to treat patients.

Sean Munro, PhD

“These uncharacterized genes have not deserved their neglect,” said Sean Munro, PhD (above), MRC Laboratory of Molecular Biology in Cambridge, England, in a press release. “Our database provides a powerful, versatile and efficient platform to identify and select important genes of unknown function for analysis, thereby accelerating the closure of the gap in biological knowledge that the unknome represents.” Clinical laboratory scientists may find the Unknome Database intriguing and useful. (Photo copyright: Royal Society.)

Risk of Ignoring Understudied Proteins

Proteomics (the study of proteins) is a rapidly advancing area of clinical laboratory testing. As genetic scientists learn more about proteins and their functions, diagnostics companies use that information to develop new assays. But did you know that researchers tend to focus on only a small fraction of the total number of protein-coding DNA sequences contained in the human genome?

The study of proteomics is primarily interested in the part of the genome that “contains instructions for building proteins … [which] are essential for development, growth, and reproduction across the entire body,” according to Scientific American. These are all protein-coding genes.

Proteomics estimates that there are more than two million proteins in the human body, which are coded for 20,000 to 25,000 genes, according to All the Science.

To build their database, the MRC researchers ranked the “unknome” proteins by how little is known about their functions in cellular processes. When they tested the database, they found some of these less-researched proteins important to biological functions such as development and stress resistance. 

“The role of thousands of human proteins remains unclear and yet research tends to focus on those that are already well understood,” said Sean Munro, PhD, MRC Laboratory of Molecular Biology in Cambridge, England, in the news release. “To help address this we created an Unknome database that ranks proteins based on how little is known about them, and then performed functional screens on a selection of these mystery proteins to demonstrate how ignorance can drive biological discovery.”

Munro created the Unknome Database along with Matthew Freeman, PhD, Head of England’s Sir William Dunn School of Pathology, University of Oxford.

In the paper, they acknowledged the human genome encodes about 20,000 proteins, and that the application of transcriptomics and proteomics has “confirmed that most of these new proteins are expressed, and the function of many of them has been identified.

“However,” the authors added, “despite over 20 years of extensive effort, there are also many others that still have no known function.”

They also recognized limited resources for research and that a preference for “relative safety” and “well-established fields” are likely holding back discoveries.

The researchers note “significant” risks to continually ignoring unexplored proteins, which may have roles in cell processes, serve as targets for therapies, and be associated with diseases as well as being “eminently druggable,” Genetic Engineering News reported.

Setting up the Unknome Database

To develop the Unknome Database, the researchers first turned to what has already come to fruition. They gave each protein in the human genome a “knownness” score based on review of existing information about “function, conservation across species, subcellular localization, and other factors,” Interesting Engineering reported.

It turns out, 3,000 groups of proteins (805 with a human protein) scored zero, “showing there’s still much to learn within the human genome,” Science News stated, adding that the Unknome Database catalogues more than 13,000 protein groups and nearly two million proteins. 

The researchers then tested the database by using it to determine what could be learned about 260 “mystery” genes in humans that are also present in Drosophila (small fruit flies).

“We used the Unknome Database to select 260 genes that appeared both highly conserved and particularly poorly understood, and then applied functional assays in whole animals that would be impractical at genome-wide scale,” the researchers wrote in PLOS Biology.

“We initially selected all genes that had a knownness score of ≤1.0 and are conserved in both humans and flies, as well as being present in at least 80% of available metazoan genome sequences. … After testing for viability, the nonessential genes were then screened with a panel of quantitative assays designed to reveal potential roles in a wide range of biological functions,” they added.

“Our screen in whole organisms reveals that, despite several decades of extensive genetic screens in Drosophila, there are many genes with essential roles that have eluded characterization,” the researchers conclude.

Clinical Laboratory Testing Using the Unknome Database

Future use of the Unknome Database may involve CRISPR technology to explore functions of unknown genes, according to the PLOS Biology paper.

Munro told Science News the research team may work with other research efforts aimed at understanding “mysterious proteins,” such as the Understudied Proteins Initiative.

The Unknome Database’s ability to be customized by others means researchers can create their own “knownness” scores as it applies to their studies. Thus, the database could be a resource in studies of treatments or medications to fight diseases, Chemistry World noted.

According to a statement prepared for Healthcare Dive by SomaLogic, a Boulder, Colorado-based protein biomarker company, diagnostic tests that measure proteins can be applied to diseases and conditions such as:

In a study published in Science Translational Medicine, SomaLogic’s SomaScan assay was reportedly successful in predicting the likelihood within four years of myocardial infarction, heart failure, stroke, and even death.

“The 27-protein model has potential as a ‘universal’ surrogate end point for cardiovascular risk,” the researchers wrote in Science Translational Medicine.

Proteomics definitely has its place in clinical laboratory testing. The development of MRC-LMB’s Unknome Database will help researchers’ increase their knowledge about the functions of more proteins which should in turn lead to new diagnostic assays for labs.

—Donna Marie Pocius

Related Information:

Mapping the ‘Unknome’ May Reveal Critical Genes Scientists Have Ignored

How Many Proteins Exist?

Unknome: A Database of Human Genes We Know Almost Nothing About

Functional Unknomics: Systematic Screening of Conserved Genes of Unknown Function

Unknome Database Ranks Proteins Based on How Little is Known about Them

How a New Database of Human Genes Can Help Discover New Biology

The Unknome Catalogs Nearly Two Million Proteins. Many are Mysterious

Into the Unknome: Scientists at MRC LMB in Cambridge Create Database Ranking Human Proteins by How Little We know About Them

Scientists Hope to Illuminate Unknown Human Proteins with New Public Database

Proteomic Tests Empower Precision Medicine

A Proteomic Surrogate for Cardiovascular Outcomes That is Sensitive to Multiple Mechanisms of Change in Risk

Stanford Researchers Discover Junk DNA Affects Gene Expression

Research findings could lead to new biomarkers for genetic tests and give clinical laboratories new capabilities to diagnose different health conditions

New insights continue to emerge about “junk DNA” (aka, non-coding DNA). For pathologists and clinical laboratories, these discoveries may have value and eventually lead to new biomarkers for genetic testing.

One recent example comes from researchers at Stanford Medicine in California who recently learned how non-coding DNA—which makes up 98% of the human genome—affects gene expression, the function that leads to observable characteristics in an organism (phenotypes).

The research also could lead to a better understanding of how short tandem repeats (STRs)—the number of times a gene is copied into RNA for protein use—affect gene expression as well, according to Stanford.

Scientists at Stowers Institute for Medical Research and Duke University School of Medicine contributed to the study.

The researchers published their findings in the journal Science titled, “Short Tandem Repeats Bind Transcription Factors to Tune Eukaryotic Gene Expression.”

Polly Fordyce, PhD

“We’ve known for a while that short tandem repeats or STRs, aren’t junk because their presence or absence correlates with changes in gene expression. But we haven’t known how they exert these effects,” said study lead Polly Fordyce, PhD (above), Associate Professor of Bioengineering and Genetics at Stanford University, in a news release. The research could lead to new clinical laboratory biomarkers for genetic testing. (Photo copyright: Stanford University.)


To Bind or Not to Bind

In their Science paper, the Stanford researchers described an opportunity to explore a new angle to transcription factors binding to some sequences, also known as sequence motifs.

“Researchers have spent a lot of time characterizing these transcription factors and figuring out which sequences—called motifs—they like to bind to the most,” said the study lead Polly Fordyce, PhD, Associate Professor of Bioengineering and Genetics at Stanford University, in a Stanford Medicine news release.

“But current models don’t adequately explain where and when transcription factors bind to non-coding DNA to regulate gene expression. Sometimes, no transcription factor is attached to something that looks like a perfect motif. Other times, transcription factors bind to stretches of DNA that aren’t motifs,” the news release explains.

Transcription factors are “like light switches that can turn genes on or off depending on what cells need,” notes a King’s College London EDIT Lab blog post.

But why do transcription factors target some places in the genome and not others?

“To solve the puzzle of why transcription factors go to some places in the genome and not to others, we needed to look beyond the highly preferred motifs,” Fordyce added. “In this study, we’re showing that the STR sequence around the motif can have a really big effect on transcription factor binding, providing clues as to what these repeated sequences might be doing.”

Such information could aid in understanding certain hereditary conditions and diseases. 

“Variations in STR length have been associated with changes in gene expression and implicated in several complex phenotypes such as schizophrenia, cancer, autism, and Crohn’s disease. However, the mechanism by which STRs affect transcription remains unknown,” the researchers wrote in Science.

Special Assays Explore Binding

According to their paper, the research team turned to the Fordyce Lab’s previously developed microfluidic binding assays (MITOMI, kMITOMI, and STAMMP) to analyze the impact of different DNA sequences on transcription factor binding.

“In the experiment we asked, ‘How do these changes impact the strength of transcription factor binding?’ We saw a surprisingly large effect. Varying the STR sequence around a motif can have a 70-fold impact on the binding,” Fordyce wrote.

In an accompanying Science article titled, “Repetitive DNA Regulates Gene Expression,” Thomas Kuhlman, PhD, Assistant Professor, Physics and Astronomy, University of California, Riverside, wrote that the study “demonstrates that STRs exert their effects by directly binding transcription factor proteins, thus explaining how STRs might influence gene expression in both normal and diseased states.”

Junk DNA Affects Blood Pressure

In another study, researchers at The Hospital for Sick Children (SickKids), which is affiliated with the University of Toronto, Ontario, examined the possible effect of non-coding DNA on genes related to blood pressure.

“This research unveils, for the first time, the intricate connection between how variants in the non-coding genome affect genes that are associated with blood pressure and with hypertension. What we’ve created is a kind of functional map of the regulators of blood pressure genes, “said Philipp Maass, PhD, Lead Researcher and Assistant Professor Molecular Genetics, University of Toronto, in a news release.

The research team used massively parallel reporter assay (MPRA) technology to analyze 4,608 genetic variants associated with blood pressure.

In “Systematic Characterization of Regulatory Variants of Blood Pressure Genes,” published in the journal Cell Genomics, the SickKids scientists noted that high throughput technology identified “regulatory variants at blood pressure loci.”

The findings could aid precision medicine for cardiovascular health and may possibly be adopted to other conditions, according to The Hospital for Sick Children.

“The variants we have characterized in the non-coding genome could be used as genomic markers for hypertension, laying the groundwork for future genetic research and potential therapeutic targets for cardiovascular disease,” Maass noted.

Why All the ‘Junk’ DNA?

Clinical laboratory scientists may wonder why genetic research has primarily focused on 20,000 genes within the genome, leaving the “junk” DNA for later investigation. So did researchers at Harvard University.

“After the Human Genome Project, scientists found that there were around 20,000 genes within the genome, a number that some researchers had already predicted. Remarkably, these genes comprise only about 1-2% of the three billion base pairs of DNA. This means that anywhere from 98-99% of our entire genome must be doing something other than coding for proteins,” they wrote in a blog post.

“Imagine being given multiple volumes of encyclopedias that contained a coherent sentence in English every 100 pages, where the rest of the space contained a smattering of uninterpretable random letters and characters. You would probably start to wonder why all those random letters and characters were there in the first place, which is the exact problem that has plagued scientists for decades,” they added.

Not only is junk DNA an interesting study subject, but ongoing research may also produce useful new biomarkers for genetic diagnostics and other clinical laboratory testing. Thus, medical lab professionals may want to keep an eye on new developments involving non-coding DNA.   

—Donna Marie Pocius

Related Information:

Stanford Medicine-led Study Clarifies How “Junk DNA” Influences Gene Expression

Short Tandem Repeats Bind Transcription Factors to Tune Eukaryotic Gene Expression

J for Junk DNA Does Not Exist!

Repetitive DNA Regulates Gene Expression

Illuminating Genetic Dark Matter: How “Junk DNA” Influences Blood Pressure

Systematic Characterization of Regulatory Variants of Blood Pressure Genes

The 99 Percent of the Human Genome

German Researchers Develop DNA Origami That Traps and Neutralizes Certain Viruses

This “Virus Trap” might eventually be manufactured by clinical laboratories for the diagnostic process

Clinical laboratory managers and pathologists will be fascinated by this new treatment coming out of Germany for viral infections. It’s an entirely different technology approach to locating and neutralizing live viruses that may eventually be able to control anti-viral-resistant strains of specific viruses as well.

As virologists and microbiologists are aware, even in our present era of technological and medical advances, viral infections are extremely difficult to treat. There are currently no effective antidotes against most viral infections and antibiotics are only successful in fighting bacterial infections.

Thus, this new technology developed by a research team at the Technical University of Munich (TUM) in Munich, Germany, that uses DNA origami to neutralize and trap viruses and render them harmless is sure to gain swift attention, especially given the world’s battle with the SARS-CoV-2 Omicron variant.

The researchers published their findings in the peer-reviewed journal Nature Materials, titled, “Programmable Icosahedral Shell System for Virus Trapping.”

Ulrike Protzer, MD

“Bacteria have a metabolism. We can attack them in different ways,” said virologist Ulrike Protzer, MD (above), Director of the Institute of Virology at TUM School of Medicine and one of the authors of the study, in a TUM press release. “Viruses, on the other hand, do not have their own metabolism, which is why antiviral drugs are almost always targeted against a specific enzyme in a single virus. Such a development takes time. If the idea of simply mechanically eliminating viruses can be realized, this would be widely applicable and thus an important breakthrough, especially for newly emerging viruses,” she added. (Photo copyright: Helmholtz Munich.)

Entrapping Viruses within 3D Hollow Structures

DNA origami is the nanoscale folding of DNA to create two- and three-dimensional complex shapes that can be manufactured with a high degree of precision at the nanoscale. Researchers have been working with and enhancing this technique for about 15 years.

However, scientists at TUM wondered if they could create such hollow structures based on the capsules that encompass viruses to entrap those viruses. They developed a method that made it possible to create artificial hollow bodies the size of a virus and explored using those hollow bodies as a type of “virus trap.”

The researchers theorized that if those hollow bodies could be lined on the inside with virus-binding molecules, they could tightly bind the viruses and remove them from circulation. For this method to be successful, however, those hollow bodies had to have large enough openings to ensure the viruses could get into the shells.

“None of the objects that we had built using DNA origami technology at that time would have been able to engulf a whole virus—they were simply too small,” said Hendrik Dietz, PhD, Professor of Physics at TUM and an author of the study in a press release. “Building stable hollow bodies of this size was a huge challenge,” he added.

So, the team of researchers used the icosahedron geometric shape, which is an object comprised of 20 sides. They engineered the hollow bodies for their virus trap from three-dimensional, triangular plates which had to have slightly beveled edges to ensure the binding points would assemble properly to the desired objects. 

“In this way, we can now program the shape and size of the desired objects using the exact shape of the triangular plates,” Dietz explained. “We can now produce objects with up to 180 subunits and achieve yields of up to 95%. The route there was, however, quite rocky, with many iterations.”

By varying the binding points on the edges of the triangles, the scientists were able to create closed hollow spheres and spheres with openings or half-shells that could be utilized as virus traps. They successfully tested their virus traps on adeno-associated viruses (AAV) and hepatitis B viruses in cell cultures.

“Even a simple half-shell of the right size shows a measurable reduction in virus activity,” Dietz stated in the press release. “If we put five binding sites for the virus on the inside—for example suitable antibodies—we can already block the virus by 80%. If we incorporate more, we achieve complete blocking.”

The team irradiated their finished building blocks with ultraviolet (UV) light and then treated the outside with polyethylene glycol and oligolysine. This process prevented the DNA particles from being immediately degraded in body fluids. Those particles were stable in mouse serum for 24 hours. The TUM scientists plan to test their building blocks on living mice soon.

“We are very confident that this material will also be well tolerated by the human body,” Dietz said.

Could Clinical Laboratories Manufacture Components of the Virus Traps?

The researchers noted that the starting materials for their virus traps can be mass produced at a very reasonable cost and may have other uses. 

“In addition to the proposed application as a virus trap, our programmable system also creates other opportunities,” Dietz said. “It would also be conceivable to use it as a multivalent antigen carrier for vaccinations, as a DNA or RNA carrier for gene therapy, or as a transport vehicle for drugs.”

There is much research yet to be done on this cutting-edge technology. However, for this therapy to be appropriate for a patient, a specimen of the virus will need to be identified and studied. Then, the DNA origami would be tailored to capture that specific virus. Thus, it’s conceivable that clinical laboratories, if used for the diagnostic step, might also be able to then manufacture the virus trap that is customized to locate, surround, and neutralize that specific virus. 

JP Schlingman

Related Information:

Engineering a Virus Trap

Programmable Icosahedral Shell System for Virus Trapping

The Virus Trap

DNA Origami

DNA Origami Hits the Big Time

Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds

Neutralizing Viruses with DNA Origami Traps

McMaster University Researchers Develop Bioinformatics ‘Shortcut’ That Speeds Detection and Identification of Pathogens, including Sepsis, SARS-CoV-2, Others

Molecular probes designed to spot minute amounts of pathogens in biological samples may aid clinical laboratories’ speed-to-answer

Driven to find a better way to isolate minute samples of pathogens from among high-volumes of other biological organisms, researchers at Canada’s McMaster University in Hamilton, Ontario, have unveiled a bioinformatics algorithm which they claim shortens time-to-answer and speeds diagnosis of deadly diseases.

Two disease pathogens the researchers specifically targeted in their study are responsible for sepsis and SARS-CoV-2, the coronavirus causing COVID-19. Clinical laboratories would welcome a technology which both shortens time-to-answer and improves diagnostic accuracy, particularly for pathogens such as sepsis and SARS-CoV-2.

Their design of molecular probes that target the genomic sequences of specific pathogens can enable diagnosticians and clinical laboratories to spot extremely small amounts of viral and bacterial pathogens in patients’ biological samples, as well as in the environment and wildlife.

“There are thousands of bacterial pathogens and being able to determine which one is present in a patient’s blood sample could lead to the correct treatment faster when time is very important,” Zachery Dickson, a lead author of the study, told Brighter World. Dickson is a bioinformatics PhD candidate in the Department of Biology at McMaster University. “The probe makes identification much faster, meaning we could potentially save people who might otherwise die,” he added.

Sepsis is a life-threatening response to infection that leads to organ failure, tissue damage, and death in hospitals worldwide. According to Sepsis Alliance, about 30% of people diagnosed with severe sepsis will die without quick and proper treatment. Thus, a “shortcut” to identifying sepsis in its early stages may well save many lives, the McMaster researchers noted.

And COVID-19 has killed millions. Such a tool that identifies sepsis and SARS-CoV-2 in minute biological samples would be a boon to hospital medical laboratories worldwide.

Hendrik Poinar, PhD

“We currently need faster, cheaper, and more succinct ways to detect pathogens in human and environmental samples that democratize the hunt, and this pipeline does exactly that,” Hendrik Poinar, PhD (above), McMaster Professor of Anthropology and a lead author of the study, told Brighter World. Poinar is Director of the McMaster University Ancient DNA Center. Hospital medical laboratories could help save many lives if sepsis and COVID-19 could be detected earlier. (Graphic copyright: McMaster University.)

Is Bioinformatics ‘Shortcut’ Faster than PCR Testing?

The National Human Genome Research Institute defines a “probe” in genetics as a “single-stranded sequence of DNA or RNA used to search for its complementary sequences in a sample genome.”

The McMaster scientists call their unique probe design process, HUBDesign, or Hierarchical Unique Bait Design. “HUB is a bioinformatics pipeline that designs probes for targeted DNA capture,” according to their paper published in the journal Cell Reports Methods, titled, “Probe Design for Simultaneous, Targeted Capture of Diverse Metagenomic Targets.”

The researchers say their probes enable a shortcut to detection—even in an infection’s early stages—by “targeting, isolating, and identifying the DNA sequences specifically and simultaneously.”

The probes’ design makes possible simultaneous targeted capture of diverse metagenomics targets, Biocompare explained.

But is it faster than PCR (polymerase chain reaction) testing?

The McMaster scientists were motivated by the “challenges of low signal, high background, and uncertain targets that plague many metagenomic sequencing efforts,” they noted in their paper.

They pointed to challenges posed by PCR testing, a popular technique used for detection of sepsis pathogens as well as, more recently, for SARS-CoV-2, the coronavirus causing COVID-19.

“The (PCR) technique relies on primers that bind to nucleic acid sequences specific to an organism or group of organisms. Although capable of sensitive, rapid detection and quantification of a particular target, PCR is limited when multiple loci are targeted by primers,” the researchers wrote in Cell Reports Methods.

According to LabMedica, “A wide array of metagenomic study efforts are hampered by the same challenge: low concentrations of targets of interest combined with overwhelming amounts of background signal. Although PCR or naive DNA capture can be used when there are a small number of organisms of interest, design challenges become untenable for large numbers of targets.”

Detecting Pathogens Faster, Cheaper, and More Accurately

As part of their study, researchers tested two probe sets:

  • one to target bacterial pathogens linked to sepsis, and
  • another to detect coronaviruses including SARS-CoV-2.

They were successful in using the probes to capture a variety of pathogens linked to sepsis and SARS-CoV-2.

“We validated HUBDesign by generating probe sets targeting the breadth of coronavirus diversity, as well as a suite of bacterial pathogens often underlying sepsis. In separate experiments demonstrating significant, simultaneous enrichment, we captured SARS-CoV-2 and HCoV-NL63 [Human coronavirus NL 63] in a human RNA background and seven bacterial strains in human blood. HUBDesign has broad applicability wherever there are multiple organisms of interest,” the researchers wrote in Cell Reports Methods.

The findings also have implications to the environment and wildlife, the researchers noted.

Of course, more research is needed to validate the tool’s usefulness in medical diagnostics. The McMaster University researchers intend to improve HUBDesign’s efficiency but note that probes cannot be designed for unknown targets.

Nevertheless, the advanced application of novel technologies to diagnose of sepsis, which causes 250,000 deaths in the US each year, according to the federal Centers for Disease Control and Prevention, is a positive development worth watching.

The McMaster scientists’ discoveries—confirmed by future research and clinical studies—could go a long way toward ending the dire effects of sepsis as well as COVID-19. That would be a welcome development, particularly for hospital-based laboratories.

—Donna Marie Pocius

Related Information:

DNA Researchers Develop Critical Shortcut to Detect and Identify Known and Emerging Pathogens

Probe Design for Simultaneous, Targeted Capture of Diverse Metagenomic Targets

New Tool Designs Probes for Targeted DNA Capture

Novel Tool Developed to Detect and Identify Pathogens

Hospitals Worldwide are Deploying Artificial Intelligence and Predictive Analytics Systems for Early Detection of Sepsis in a Trend That Could Help Clinical Laboratories Microbiologists

Penn Medicine Informatics Taps Medical Laboratory Data and Three Million Patient Records Over 10 Years to Evaluate Patients’ Sepsis Risk and Head Off Heart Failure

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