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Clinical Laboratories and Pathology Groups

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Advancements That Could Bring Proteomics and Mass Spectrometry to Clinical Laboratories

Experts list the top challenges facing widespread adoption of proteomics in the medical laboratory industry

Year-by-year, clinical laboratories find new ways to use mass spectrometry to analyze clinical specimens, producing results that may be more precise than test results produced by other methodologies. This is particularly true in the field of proteomics.

However, though mass spectrometry is highly accurate and fast, taking only minutes to convert a specimen into a result, it is not fully automated and requires skilled technologists to operate the instruments.

Thus, although the science of proteomics is advancing quickly, the average pathology laboratory isn’t likely to be using mass spectrometry tools any time soon. Nevertheless, medical laboratory scientists are keenly interested in adapting mass spectrometry to medical lab test technology for a growing number of assays.

Molly Campbell, Science Writer and Editor in Genomics, Proteomics, Metabolomics, and Biopharma at Technology Networks, asked proteomics experts “what, in their opinion, are the greatest challenges currently existing in proteomics, and how can we look to overcome them?” Here’s a synopsis of their answers:

Lack of High Throughput Impacts Commercialization

Proteomics isn’t as efficient as it needs to be to be adopted at the commercial level. It’s not as efficient as its cousin genomics. For it to become sufficiently efficient, manufacturers must be involved.

John Yates III, PhD, Professor, Department of Molecular Medicine at Scripps Research California campus, told Technology Networks, “One of the complaints from funding agencies is that you can sequence literally thousands of genomes very quickly, but you can’t do the same in proteomics. There’s a push to try to increase the throughput of proteomics so that we are more compatible with genomics.”

For that to happen, Yates says manufacturers need to continue advancing the technology. Much of the research is happening at universities and in the academic realm. But with commercialization comes standardization and quality control.

“It’s always exciting when you go to ASMS [the conference for the American Society for Mass Spectrometry] to see what instruments or technologies are going to be introduced by manufacturers,” Yates said.

There are signs that commercialization isn’t far off. SomaLogic, a privately-owned American protein biomarker discovery and clinical diagnostics company located in Boulder, Colo., has reached the commercialization stage for a proteomics assay platform called SomaScan. “We’ll be able to supplant, in some cases, expensive diagnostic modalities simply from a blood test,” Roy Smythe, MD, CEO of SomaLogic, told Techonomy.


The graphic above illustrates the progression mass spectrometry took during its development, starting with small proteins (left) to supramolecular complexes of intact virus particles (center) and bacteriophages (right). Because of these developments, today’s medical laboratories have more assays that utilize mass spectrometry. (Photo copyright: Technology Networks/Heck laboratory, Utrecht University, the Netherlands.)

Achieving the Necessary Technical Skillset

One of the main reasons mass spectrometry is not more widely used is that it requires technical skill that not many professionals possess. “For a long time, MS-based proteomic analyses were technically demanding at various levels, including sample processing, separation science, MS and the analysis of the spectra with respect to sequence, abundance and modification-states of peptides and proteins and false discovery rate (FDR) considerations,” Ruedi Aebersold, PhD, Professor of Systems Biology at the Institute of Molecular Systems Biology (IMSB) at ETH Zurich, told Technology Networks.

Aebersold goes on to say that he thinks this specific challenge is nearing resolution. He says that, by removing the problem created by the need for technical skill, those who study proteomics will be able to “more strongly focus on creating interesting new biological or clinical research questions and experimental design.”

Yates agrees. In a paper titled, “Recent Technical Advances in Proteomics,” published in F1000 Research, a peer-reviewed open research publishing platform for scientists, scholars, and clinicians, he wrote, “Mass spectrometry is one of the key technologies of proteomics, and over the last decade important technical advances in mass spectrometry have driven an increased capability of proteomic discovery. In addition, new methods to capture important biological information have been developed to take advantage of improving proteomic tools.”

No High-Profile Projects to Stimulate Interest

Genomics had the Human Genome Project (HGP), which sparked public interest and attracted significant funding. One of the big challenges facing proteomics is that there are no similarly big, imagination-stimulating projects. The work is important and will result in advances that will be well-received, however, the field itself is complex and difficult to explain.

Emanuel Petricoin, PhD, is a professor and co-director of the Center for Applied Proteomics and Molecular Medicine at George Mason University. He told Technology Networks, “the field itself hasn’t yet identified or grabbed onto a specific ‘moon-shot’ project. For example, there will be no equivalent to the human genome project, the proteomics field just doesn’t have that.”

He added, “The equipment needs to be in the background and what you are doing with it needs to be in the foreground, as is what happened in the genomics space. If it’s just about the machinery, then proteomics will always be a ‘poor step-child’ to genomics.”

Democratizing Proteomics

Alexander Makarov, PhD, is Director of Research in Life Sciences Mass Spectrometry (MS) at Thermo Fisher Scientific. He told Technology Networks that as mass spectrometry grew into the industry we have today, “each new development required larger and larger research and development teams to match the increasing complexity of instruments and the skyrocketing importance of software at all levels, from firmware to application. All this extends the cycle time of each innovation and also forces [researchers] to concentrate on solutions that address the most pressing needs of the scientific community.”

Makarov describes this change as “the increasing democratization of MS,” and says that it “brings with it new requirements for instruments, such as far greater robustness and ease-of-use, which need to be balanced against some aspects of performance.”

One example of the increasing democratization of MS may be several public proteomic datasets available to scientists. In European Pharmaceutical Review, Juan Antonio Viscaíno, PhD, Proteomics Team Leader at the European Bioinformatics Institute (EMBL-EBI) wrote, “These datasets are increasingly reused for multiple applications, which contribute to improving our understanding of cell biology through proteomics data.”

Sparse Data and Difficulty Measuring It

Evangelia Petsalaki, PhD, Group Leader EMBL-EBI, told Technology Networks there are two related challenges in handling proteomic data. First, the data is “very sparse” and second “[researchers] have trouble measuring low abundance proteins.”

Petsalaki notes, “every time we take a measurement, we sample different parts of the proteome or phosphoproteome and we are usually missing low abundance players that are often the most important ones, such as transcription factors.” She added that in her group they take steps to mitigate those problems.

“However, with the advances in MS technologies developed by many companies and groups around the world … and other emerging technologies that promise to allow ‘sequencing’ proteomes, analogous to genomes … I expect that these will not be issues for very long.”

So, what does all this mean for clinical laboratories? At the current pace of development, its likely assays based on proteomics could become more common in the near future. And, if throughput and commercialization ever match that of genomics, mass spectrometry and other proteomics tools could become a standard technology for pathology laboratories.

—Dava Stewart

Related Information:

5 Key Challenges in Proteomics, As Told by the Experts

The Evolution of Proteomics—Professor John Yates

The Evolution of Proteomics—Professor Ruedi Aebersold

The Evolution of Proteomics—Professor Emanuel Petricoin

The Evolution of Proteomics—Professor Alexander Makarov

The Evolution of Proteomics—Dr. Evangelia Petsalaki

For a Clear Read on Our Health, Look to Proteomics

Recent Technical Advances in Proteomics

Emerging Applications in Clinical Mass Spectrometry

HPP Human Proteome Project

Open Data Policies in Proteomics Are Starting to Revolutionize the Field

Native Mass Spectrometry: A Glimpse Into the Machinations of Biology

University of Edinburgh Study Finds Antimicrobial Bacteria in Hospital Wastewater in Research That Has Implications for Microbiologists

The highly infectious bacteria can survive treatment at local sewage plants and enter the food chain of surrounding populations, the study revealed

Researchers at the University of Edinburgh (UE) in Scotland found large amounts of antimicrobial-resistance (AMR) genes in hospital wastewater. These findings will be of interest to microbiologists and clinical laboratory managers, as the scientists used metagenomics to learn “how abundances of AMR genes in hospital wastewater are related to clinical activity.”

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.

Using Metagenomics to Surveille Hospital Patients

Antimicrobial resistance is creating super bacteria that are linked to increases in hospital-acquired infections (HAIs) nationwide. Dark Daily has reported many times on the growing danger of deadly antimicrobial resistant “super bugs,” which also have been found in hospital ICUs (see “Potentially Fatal Fungus Invades Hospitals and Public Is Not Informed,” August 26, 2019.)

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.”

AMR bacteria also are being spread by human touch throughout city subways, bus terminals, and mass transportation, making it difficult for the Centers for Disease Control and Prevention (CDC) to identify the source of the outbreak and track and contain it. This has led microbiologists to conduct similar studies using genetic sequencing to identify ways to track pathogens through city infrastructures and transportation systems. (See, “Microbiologists at Weill Cornell Use Next-Generation Gene Sequencing to Map the Microbiome of New York City Subways,” December 13, 2013.)

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;
  • Finally, they complete the genetic sequencing on an Illumina HiSeq4000 System.

The researchers reported these findings:

  • 181 clinical isolates were identified in the samples of wastewater;
  • 1,047 unique bacterial genes were detected across all samples;
  • 19 genes made up more than 60% of bacteria in samples;
  • Overriding bacteria identified as Pseudomonas and Acinetobacter environmental samples (Pseudomonas fluorescens and Acinetobacter johnsonii) were most likely from hospital pipes;
  • Gut-related bacteria—Faecalibacterium, Bacteroides, Bifidobacterium, and Escherichia, were more prevalent in the hospital samples than in those from the community;
  • 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.  

—Donna Marie Pocius

Related Information:

Secrets of the Hospital Underbelly: Abundance of Antimicrobial-Resistance Genes in Hospital Wastewater Reflects Hospital Microbial Use and Inpatient Length of Stay

Antibiotic-Resistance Genes Trouble Hospital Water; Study Emphasizes Importance of Antibiotic Stewardship Programs, Expert Says

Fact Sheet: Antibiotic Resistance

United States Gathers 350 Commitments to Combat Antibiotic Resistance, Action Must Continue

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenemase Resistance

Dark Daily E-briefings: Hospital-Acquired Infections

NIH Study Reveals Surprising New Source of Antibiotic Resistance that Will Interest Microbiologists and Medical Laboratory Scientists

University of Washington and Microsoft Research Encode Data into DNA, Demonstrating Potential New Use for Genetic Sequences

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.

The MR/UW team published their findings in Nature Scientific Reports.

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.

—Dava Stewart

Related Information:

With a “Hello,” Microsoft and UW Demonstrate First Fully Automated DNA Data Storage

Demonstration of End-to-End Automation of DNA Data Storage

UW Team Stores Digital Images in DNA—and Retrieves Them Perfectly

Microsoft and UW Demonstrate First Fully Automated DNA Data Storage

Storing Data in DNA Is A Lot Easier than Getting It Back Out

DNA Could Store All of the World’s Data in One Room

The Rise of DNA Data Storage

Forget Silicon—SQL On DNA Is the Next Frontier for Databases

Fortune Magazine Offers 10 Healthcare Predictions for 2019, Several Trends Will Pressure Clinical Laboratories and Anatomic Pathology Groups

Following two partially successful years of predictions, a pair of venture capitalists look into their crystal ball and share another batch of predictions for the coming year

Healthcare has its fair share of fortune tellers. Rarely are they consistent. However, the predictions of two healthcare investors in California have been so accurate that Fortune magazine now publishes an article each year featuring the duo’s Top Healthcare Predictions.

These predictions will be of interest to clinical laboratory managers and pathologists because several describe the changes coming to the hospitals, physicians, and health insurers who use and pay for medical laboratory tests.

The two individuals with the crystal ball are Bob Kocher, MD, and Bryan Roberts, PhD. Both are healthcare investors and partners at Venrock, a silicon-valley venture capital firm located in Palo Alto, Calif. They’ve been making fairly accurate predictions for the past few years.

Here are their predictions for healthcare in 2019:

  • More payer consolidation: The authors foresee that the largest health insurance companies with low administrative costs and high profit margins will become more competitive in obtaining clients. This type of competition could force smaller payers to struggle to gain and retain national accounts and have difficulty competing in the Medicare Advantage and Medicaid markets. They also anticipate “the growth of Medicaid, with several states electing to expand, and Medicare Advantage will also trigger [mergers and acquisitions] in order to enter these growing and more profitable market segments.”

If small health plans are acquired and merged, clinical laboratories and anatomic pathology groups could lose access to patients because the biggest payers have narrow networks and favor the national labs. 

  • Physician-led Accountable Care Organizations (ACOs) will grow rapidly: Their prediction is that primary care doctors will realize they can make more money and have more successful practices if they detach from hospitals and create independent businesses. With Medicare’s latest ACO regulations favoring doctor-led accountable care organizations over hospital-led ACOs, physicians may find it easier to expand independent practices.

If this prediction comes to fruition, small local medical laboratories may be able to reap the benefits of an increase in the number of physician-led ACOs by delivering enriched data and analytical services to those practices.

  • Doctors get less dissatisfied: Kocher and Roberts feel that health systems have listened to the complaints from doctors about their bad experiences using electronic health records (EHRs) and will take the necessary steps to ensure physicians are more satisfied with their EHR experiences. New innovations like machine learning and improvement in voice interfaces should help ease the burden of physicians when using EHRs. Improved voice technology can reduce the time doctors spend typing, clicking, and searching in their databases. The authors noted that “it may be easier to use voice for healthcare than for consumer applications since the vocabulary is smaller and context is far more predictable.” 
  • Interoperability becomes interoperable: EHRs will start to better communicate with each other across different health systems. The Centers for Medicare and Medicaid Services (CMS) Patients Over Paperwork initiative is intended to help states that are “pushing for connectivity as one tactic to address the opioid epidemic and to improve resiliency from natural disasters, necessitating the need to access data.” 

This prediction could be favorable for clinical laboratories and pathology groups that must create and support interfaces between their laboratory information management system (LIMS) and outside EHRs.

  • Consolidation in digital health: The authors predict that “growth equity will get tighter in 2019 for small companies that have not achieved product market fit” which “will lead to a flurry of consolidation into platforms.” They also forecast that large healthcare employers may transition from being the early adopters of digital platforms to relying on the advice of partners who have already been using those platforms in their businesses.

The authors of the top-10 list are Bob Kocher, MD (left) and Bryan Roberts, PhD (right), healthcare investors and partners at Venrock, a venture capital firm located in Palo Alto, CA.
(Photos copyright: Venrock.)
  • InsureTech takes a lump or two: InsureTech—a portmanteau from the words insurance and technology—as a business sector, may have some setbacks with payers examining and auditing charts more closely for errors and issuing fines accordingly. The practice of upcoding—where a biller assigns a medical code for a more expensive service or procedure than the one that was actually performed—is emerging as an area of risk for providers using the capabilities of InsureTech products and services. CMS actually has a “coding intensity adjustment” in place when reimbursing for Medicare Advantage claims because upcoding has become so prevalent. 
  • Dialysis disrupted: Dialysis centers will become less plentiful as more patients opt to have their blood cleansed at home. Studies have shown that self-serve dialysis in the home can be safer, more reliable, and less expensive than traditional dialysis centers. Advantages of home dialysis include fewer trips to dialysis centers, more flexible scheduling for treatments, increased privacy, less dietary restrictions, and less problems with the fistula or graft area.

According to the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), there are more than 661,000 people living with kidney failure or end stage renal disease (ESRD) in the US. Approximately 468,000 of those individuals rely on dialysis to rid toxins and excess fluid from their blood and only about eight percent of those individuals were using home dialysis machines in 2016, Yahoo News noted.

  • Telemedicine takes off: The authors expect telemedicine usage will more than double in 2019 as more payers, healthcare providers, and patients recognize its benefits. More health plans, including Medicare, are adding billing codes to reimburse patients for telemedicine visits with their healthcare providers. Becker’s Hospital Review in 2016 predicted that seven million people would be using telemedicine services by 2018.
  • PBM disruption talk becomes reality: The authors “expect next generation pharmacy supply ecosystem efforts to gain real traction in 2019.” Third-party administrators of prescription drug programs for health insurance plans, known as Pharmacy Benefit Managers (PBMs) will be scrutinized by the government in an effort to determine why drug costs are so high and to find ways those costs can be lowered. As pharmaceutical companies continue to aggressively raise prices for their products, patients are paying more for their medications and intermediaries are reaping the financial rewards. Drugs are currently being marked up an average of 40% by the distribution system, according to Fortune.
  • Real progress with new DNA sequencing platforms: Kocher and Roberts see the emergence of new Deoxyribonucleic acid (DNA) sequencing applications and platforms being developed and released into the market. These new technologies could lead to less expensive costs for sequencing services and more competition among genomics companies. This will be a favorable development for clinical laboratories and pathology groups because it will make gene sequencing cheaper, faster, and more accurate.

Fortune is a business magazine, headquartered in New York City, that publishes feature articles on multinational business topics as well as popular ranked lists, including the Fortune 500 list which annually ranks companies by revenue.

Given the track record of the two experts making these predictions, it would be appropriate for the business leaders of clinical labs and pathology groups to consider how each prediction may change how the providers and payers they serve use lab testing services and pay for same. 

—JP Schlingman

Related Information:

10 Health Care Predictions for 2019 from a Pair of Venture Gurus

Telemedicine to Attract 7M Patient Users by 2018—12 Statistics on the Thriving Market

Researchers at University of British Columbia Use Human Gut Bacteria to Convert A/B Blood into Universal Type-O

If this technology proves viable on large scale, medical laboratories in hospitals that manage blood banks could have larger supplies of universal blood units

Once again, the amazing human microbiome is at the heart of a new scientific breakthrough that could offer new tools for clinical laboratories and provide much needed resources to emergency departments and hospitals.

Canadian researchers at the University of British Columbia (UBC) in Vancouver have discovered a microbe in the human gut they believe is capable of converting donor blood into “universal” type-O blood.

“We have been particularly interested in enzymes that allow us to remove the A or B antigens from red blood cells. If you can remove those antigens, which are just simple sugars, then you can convert A or B to O blood,” Stephen Withers, PhD, a professor and biochemist at UBC explained in an American Chemical Society (ACS) news release.

Such a breakthrough would be game-changing not only for emergency departments that rely on much-needed supplies of universal-donor blood, but also for the medical laboratories that run most hospital blood banks.

Uncovering a method to transform type A blood into type O would greatly enlarge the current blood supply because type-O blood can be donated to patients regardless of which of the four main blood groups they belong to—O, A, B, or AB.

This is yet another addition to a growing list of discoveries involving human gut bacteria that Dark Daily has reported on in past years.

Withers presented his research at the 256th National Meeting and Exposition of the American Chemical Society 2018 annual meeting in Boston. Click here to watch a video of his presentation.

Using Metagenomics to Convert A/B Blood to Type O

UBC scientists relied on metagenomics—a technique that enables researchers to study microbial communities using DNA sequencing—to investigate enzymes that potentially could destroy all the A and B antigens from red blood cells, thereby converting type A and B blood into Type O universal blood.

“With metagenomics, you take all of the organisms from an environment and extract the sum total DNA of those organisms all mixed up together,” Withers said in the ACS news release. 

Withers’ team considered sampling DNA from mosquitoes and leaches but ultimately turned to the human body, where they found successful candidate enzymes in the gut microbiota. They focused on glycosylated proteins called mucins that line the gut wall, providing sugars that serve as attachment points for gut bacteria, while also feeding them as they aid in digestion, the ACS report noted.

“By honing in on the bacteria feeding on those sugars, we isolated the enzymes the bacteria use to pluck off the sugar molecules,” Withers said in a UBC statement. “We then produced quantities of those enzymes through cloning and found that they were capable of performing a similar action on blood antigens.”

Although enzymes long have been considered a key to transforming donated blood to a common type, the gut enzymes the UBC team identified are 30 times more efficient at removing red blood cell antigens than previously studied enzymes, the ACS news release noted. Their findings demonstrate once again how the human microbiome is intertwined with many processes happening within the body, opening the possibility of future novel uses of enzymes.

“Researchers have been studying the use of enzymes to modify blood as far back as 1982. However, these new enzymes can do the job 30 times better,” Stephen Withers, PhD (above), Professor and biochemist at the University of British Columbia, noted in the UBC statement. Should his technique for converting A and B blood types to type O prove successful on a large scale, emergency departments and medical laboratories that manage blood banks could finally gain a dependable source of blood. (Photo copyright: University of British Columbia.)

Zuri Sullivan, an immunologist and PhD candidate at Yale University, believes the blood-converting enzymes discovered by the USB team may be the first of many discoveries revealed as researchers investigate the untapped potential of the gut microbiome to solve medical challenges.

“The premise here is really powerful. There’s an untapped genetic resource in the [genes] encoded by the gut microbiome,” she told Smithsonian Magazine.

Researchers Have High Hopes but More Testing Is Needed

According to the UBC statement, Withers and UBC colleagues microbiologist Steven Hallam, PhD, and pathologist Jay Kizhakkedathu, PhD, of the UBC Center for Blood Research, are applying for a patent on the new enzymes, while working to validate the enzymes and test them on a larger scale in preparation for clinical testing.

In addition, the ACS news release notes that the UBC team “plans to carry out directed evolution, a protein engineering technique that simulates natural evolution, with the goal of creating the most efficient sugar-removing enzyme.”

“I am optimistic that we have a very interesting candidate to adjust donated blood to a common type,” Withers said in the ACS statement. “Of course, it will have to go through lots of clinical trials to make sure that it doesn’t have any adverse consequences, but it is looking very promising.”

Fortune health journalist Sy Mukherjee praised the UBC discovery, but warned against “coming to any overhyped conclusions” until more testing is done.

“But if it’s a sustainable technique, the implications are multifold,” he noted. “Especially given the nature of the technique itself, which involves lopping off certain antigens (which are, in essence, simple sugars) from particular red blood cells. The question is whether it can be used on a wide-scale in a safe and efficient manner to create larger blood supplies in times of need.”

That certainly is the question. For decades, scientists have searched for the secret to creating universal blood and now it appears the answer may have been lurking inside our bodies all along. Clinical laboratories may soon see human microbiome become linked to even more discoveries that lead to new tests and diagnostic tools.

—Andrea Downing Peck

Related Information:

Gut Bacteria Provide Key to Making Universal Blood

Gut Enzymes Could Hold Key to Producing Universal Blood

What’s the Most Common Blood Type?

In the Quest for Universal Blood, Go with Your Gut

Brainstorm Health: Changing Blood Types, Exact Sciences Pfizer Deal, Israel Bans Juul

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