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Clinical Laboratories and Pathology Groups

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Clinical Laboratories and Pathology Groups

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Scientists Close in on Elusive Goal of Adapting Nanopore Technology for Protein Sequencing

Technology could enable medical laboratories to deploy inexpensive protein sequencing with a handheld device at point of care and remote locations

Clinical laboratories engaged in protein testing will be interested in several recent studies that suggest scientists may be close to adapting nanopore-sensing technology for use in protein identification and sequencing. The new proteomics techniques could lead to new handheld devices capable of genetic sequencing of proteins at low cost and with a high degree of sensitivity, in contrast to current approaches based on mass spectrometry.

But there are challenges to overcome, not the least of which is getting the proteins to cooperate. Compact devices based on nanopore technology already exist that can sequence DNA and RNA. But “there are lots of challenges with proteins” that have made it difficult to adapt the technology, Aleksei Aksimentiev, PhD, Professor of Biological Physics at the University of Illinois at Urbana-Champaign, told ASBMB Today, a publication of the American Society for Biochemistry and Molecular Biology. “In particular, they’re not uniformly charged; they’re not linear, most of the time they’re folded; and there are 20 amino acids, plus a zoo of post-translational modifications,” he added.

The ASBMB story notes that nanopore technology depends on differences in charges on either side of the membrane to force DNA or RNA through the hole. This is one reason why proteins pose such a challenge.

Giovanni Maglia, PhD, a Full Professor at the University of Groningen in the Netherlands and researcher into the fundamental properties of membrane proteins and their applications in nanobiotechnology, says he has developed a technique that overcomes these challenges.

“Think of a cell as a miniature city, with proteins as its inhabitants. Each protein-resident has a unique identity, its own characteristics, and function. If there was a database cataloging the fingerprints, job profiles, and talents of the city’s inhabitants, such a database would undoubtedly be invaluable!” said Behzad Mehrafrooz, PhD (above), Graduate Research Assistant at University of Illinois at Urbana-Champaign in an article he penned for the university website. This research should be of interest to the many clinical laboratories that do protein testing. (Photo copyright: University of Illinois.)

How the Maglia Process Works

In a Groningen University news story, Maglia said protein is “like cooked spaghetti. These long strands want to be disorganized. They do not want to be pushed through this tiny hole.”

His technique, developed in collaboration with researchers at the University of Rome Tor Vergata, uses electrically charged ions to drag the protein through the hole.

“We didn’t know whether the flow would be strong enough,” Maglia stated in the news story. “Furthermore, these ions want to move both ways, but by attaching a lot of charge on the nanopore itself, we were able to make it directional.”

The researchers tested the technology on what Maglia described as a “difficult protein” with many negative charges that would tend to make it resistant to flow.

“Previously, only easy-to-thread proteins were analyzed,” he said in the news story. “But we gave ourselves one of the most difficult proteins as a test. And it worked!”

Maglia now says that he intends to commercialize the technology through a new startup called Portal Biotech.

The Groningen University scientists published their findings in the journal Nature Biotechnology, titled “Translocation of Linearized Full-Length Proteins through an Engineered Nanopore under Opposing Electrophoretic Force.”

Detecting Post-Translational Modifications in the UK

In another recent study, researchers at the University of Oxford reported that they have adapted nanopore technology to detect post-translational modifications (PTMs) in protein chains. The term refers to changes made to proteins after they have been transcribed from DNA, explained an Oxford news story.

“The ability to pinpoint and identify post-translational modifications and other protein variations at the single-molecule level holds immense promise for advancing our understanding of cellular functions and molecular interactions,” said contributing author Hagan Bayley, PhD, Professor of Chemical Biology at University of Oxford, in the news story. “It may also open new avenues for personalized medicine, diagnostics, and therapeutic interventions.”

Bayley is the founder of Oxford Nanopore Technologies, a genetic sequencing company in the UK that develops and markets nanopore sequencing products.

The news story notes that the new technique could be integrated into existing nanopore sequencing devices. “This could facilitate point-of-care diagnostics, enabling the personalized detection of specific protein variants associated with diseases including cancer and neurodegenerative disorders,” the story states.

The Oxford researchers published their study’s findings in the journal Nature Nanotechnology titled, “Enzyme-less Nanopore Detection of Post-Translational Modifications within Long Polypeptides.”

Promise of Nanopore Protein Sequencing Technology

In another recent study, researchers at the University of Washington reported that they have developed their own method for protein sequencing with nanopore technology.

“We hacked the [Oxford Nanopore] sequencer to read amino acids and PTMs along protein strands,” wrote Keisuke Motone, PhD, one of the study authors in a post on X (formerly Twitter) following the study’s publication on the preprint server bioRxiv titled, “Multi-Pass, Single-Molecule Nanopore Reading of Long Protein Strands with Single-Amino Acid Sensitivity.”

“This opens up the possibility for barcode sequencing at the protein level for highly multiplexed assays, PTM monitoring, and protein identification!” Motone wrote.

In a commentary they penned for Nature Methods titled, “Not If But When Nanopore Protein Sequencing Meets Single-Cell Proteomics,” Motone and colleague Jeff Nivala, PhD, Principal Investigator at University of Washington, pointed to the promise of the technology.

Single-cell proteomics, enabled by nanopore protein sequencing technology, “could provide higher sensitivity and wider throughput, digital quantification, and novel data modalities compared to the current gold standard of protein MS [mass spectrometry],” they wrote. “The accessibility of these tools to a broader range of researchers and clinicians is also expected to increase with simpler instrumentation, less expertise needed, and lower costs.”

There are approximately 20,000 human genes. However, there are many more proteins. Thus, there is strong interest in understanding the human proteome and the role it plays in health and disease.

Technology that makes protein testing faster, more accurate, and less costly—especially with a handheld analyzer—would be a boon to the study of proteomics. And it would give clinical laboratories new diagnostic tools and bring some of that testing to point-of-care settings like doctor’s offices.

—Stephen Beale

Related Information:

Nanopores as the Missing Link to Next Generation Protein Sequencing

Nanopore Technology Achieves Breakthrough in Protein Variant Detection

The Scramble for Protein Nanopore Sequencing

The Emerging Landscape of Single-Molecule Protein Sequencing Technologies

ASU Researcher Advances the Science of Protein Sequencing with NIH Innovator Award          

The Missing Link to Make Easy Protein Sequencing Possible?

Engineered Nanopore Translocates Full Length Proteins

Not If But When Nanopore Protein Sequencing Meets Single-Cell Proteomics

Enzyme-Less Nanopore Detection of Post-Translational Modifications within Long Polypeptides

Unidirectional Single-File Transport of Full-Length Proteins through a Nanopore

Translocation of Linearized Full-Length Proteins through an Engineered Nanopore under Opposing Electrophoretic Force

Interpreting and Modeling Nanopore Ionic Current Signals During Unfoldase-Mediated Translocation of Single Protein Molecules

Multi-Pass, Single-Molecule Nanopore Reading of Long Protein Strands with Single-Amino Acid Sensitivity

University of Illinois Study Concludes Regular Physical Exercise Improves Human Microbiome; Might Be Useful Component of New Treatment Regimens for Cancer and Other Chronic Diseases

Exercise contributes to improving the human microbiome in ways that fight disease and clinical labs might eventually provide tests that help track beneficial changes in a patient’s microbiome

With growing regularity, new discoveries about the human Microbiome have been reported in scientific journals and the media. Some of these discoveries have led to innovations in clinical laboratory tests over the past few years. Dark Daily reported on these breakthroughs, which include: improved cancer drugs, life extension, personalized medical treatments (AKA, precision medicine), genetic databases, and women’s health.

Now, a study from the University of Illinois at Urbana-Champaign (UI) has linked exercise to beneficial changes in the makeup of human microbiota. The researchers identified significant differences in the gut bacteria of obese and lean individuals who underwent the same endurance training. The lean individuals developed healthy gut bacteria at a much higher rate than the obese participants. And they retained it, so long as the exercise continued.

Thus, researchers believe weight loss and regular exercise could become critical components of new treatment regimens for many chronic diseases, including cancer.

Regular Exercise Increases Good Gut Bacteria in Humans and Mice

The UI researchers published the results of their study in Medicine and Science in Sports and Exercise, a journal of the American College of Sports Medicine. To perform their study, they analyzed the impact six weeks of endurance training had on the gut bacteria of 32 adults:

  • Eighteen of the subjects were lean and the remaining 14 were obese;
  • Eleven of the obese and nine of the lean participants were female; and,
  • All 32 were sedentary before the study began.

The subjects participated in six weeks of supervised exercise three days/week. They started at 30-minutes/day and progressed to 60-minutes/day. Fecal samples were collected from the participants before and after the six weeks of training. The subjects were instructed to not change any of their dietary habits during the study.

Upon completion of the initial six-week exercise program, participants returned to a sedentary lifestyle for another six weeks and then researchers took more fecal samples.

Jacob Allen, PhD-Candidate (left), and Jeffrey Woods, PhD

In a University of Illinois study, Jacob Allen, PhD-Candidate (left), and Jeffrey Woods, PhD (right), et al, concluded that regular exercise increased production of beneficial gut bacterial (microbiome) more in lean individuals than in obese participants. This finding could alter how anatomic pathologists and medical laboratories view exercise and weight loss for patients undergoing treatment regimens for chronic diseases. (Photo copyright: University of Illinois/L. Brian Stauffer.)

As a result of the study, the researchers found the gut bacteria of the subjects did change, however, those changes varied among the participants. Fecal concentrations of short chain fatty acids (SCFAs), particularly butyrate, increased in the guts of the lean participants but not in the guts of the obese subjects.

SCFAs have been shown to improve metabolism and reduce inflammation in the body, and they are the main source of energy for the cells lining the colon. However, nearly all of the beneficial changes in the participants’ gut bacteria disappeared after six weeks of non-exercise.

“The bottom line is that there are clear differences in how the microbiome of somebody who is obese versus somebody who is lean responds to exercise,” Jeffrey Woods, PhD, Professor, Department of Kinesiology and Community Health, College of Applied Health Sciences, University of Illinois at Urbana-Champaign and co-leader of the study, told UI’s News Bureau. “These are the first studies to show that exercise can have an effect on your gut independent of diet or other factors.”

Reduced Inflammation Promotes Healing

The researchers had previously performed a related study using lab mice and found similar results. For that experiment, mice were separated into two groups where some were permitted to run around and be active while the others were sedentary. The gut material from all of the mice was then transplanted into gnotobiotic (germ-free) mice where their microbiomes were exposed to a substance that was known to cause irritation and inflammation in the colon. The animals with the gut bugs from the active mice experienced less inflammation and were better than the sedentary mice at resisting and healing tissue damage.

“We found that the animals that received the exercised microbiota had an attenuated response to a colitis-inducing chemical,” Jacob Allen, PhD Candidate, co-leader of the study and former doctoral student at UI, now a postdoctoral researcher at Nationwide Children’s Hospital in Columbus, Ohio, told the UI News Bureau. “There was a reduction in inflammation and an increase in the regenerative molecules that promote a faster recovery.”

Exercise Added to Growing List of Benefits from Health Gut Bacteria

Similar research in the past has found that healthy gut bacteria may have many positive effects on the body, including:

  • Improved immune health;
  • Improved mood and mental health;
  • Boosting energy levels;
  • Improved cholesterol levels;
  • Regulated hormone levels;
  • Reduction of yeast infections;
  • Healthy weight support;
  • Improved oral health; and,
  • Increased life expectancy.

Other ways to improve gut bacteria include: dietary changes, taking probiotics, lowering stress levels, and getting enough sleep. Now regular exercise can be added to this growing list.

Once further research confirms the findings of this study and useful therapies are developed from this knowledge, clinical laboratories should be able to provide microbiome testing that would help physicians and patients track the benefits of exercise on enhancing gut bacteria.

—JP Schlingman

Related Information:

Exercise Alters Our Microbiome. Is That One Reason It’s So Good for Us?

Exercise Training-induced Modification of the Gut Microbiota Persists After Microbiota Colonization and Attenuates the Response to Chemically-induced Colitis in Gnotobiotic Mice

Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans

Exercise Changes Gut Microbial Composition Independent of Diet, Team Reports

Exercise Can Beneficially Alter the Composition of Your Gut Microbiome

Researchers Discover Link between Gut Bacteria and the Effectiveness of Certain Cancer Drugs; Knowledge May Lead to New Types of Clinical Laboratory Tests

Researchers in Two Separate Studies Discover Gut Microbiome Can Affect Efficacy of Certain Cancer Drugs; Will Findings Lead to a New Clinical Laboratory Test?

Attention Microbiologists and Medical Laboratory Scientists: New Research Suggests an Organism’s Microbiome Might Be a Factor in Longer, More Active Lives

Get the Poop on Organisms Living in Your Gut with a New Consumer Laboratory Test Offered by American Gut and uBiome

Mayo Clinic and Whole Biome Announce Collaboration to Research the Role of the Human Microbiome in Women’s Diseases Using Unique Medical Laboratory Tests

In the Field of Nano-Scale Diagnostics, Many Researchers Are Developing ‘Lab-on-Skin’ Technologies That Can Monitor Many Clinical Laboratory Biomarkers

Lab-on-skin is the latest concept to join the lab-on-a-chip, lab-in-a-needle, and lab-on-paper field, as researchers continue to seek ways to miniaturize medical laboratory tests

Move over, lab-on-a-chip and lab-on-paper. There’s a new diagnostic technology in research labs that is gaining credibility. It is called lab-on-skin technology and some scientists are quite excited about how it might be used for a variety of clinical purposes.

A recent story published in ACS Nano titled, “Lab-on-Skin: A Review of Flexible and Stretchable Electronics for Wearable Health Monitoring,” reviews the latest advancements in lab-on-skin technology. It provides an overview of different research initiatives incorporating lab-on-skin technologies.

From telehealth to precision medicine to point-of-care mobile devices, anatomic pathologist and clinical laboratories are about to be challenged with new diagnostic technologies. These technologies are intended to streamline the workflow between physicians and medical laboratories while improving access to patient data and medical laboratory test results.

Of all the mobile devices designed to support medical care, no technology may have more potential to change the pathology profession than nanotechnology-based diagnostic devices. Whether lab-on-a-chip, lab-in-a-needle, or lab-on-paper, these miniature laboratories are so small dozens can be carried in a pocket.

Most importantly, for certain diagnostic tests, some of these devices being developed hope to deliver full-size-lab quality results accurately and inexpensively, even in rural regions and areas with little or no resources, such as electricity or water. (See Dark Daily, “Lab-on-a-Chip Diagnostics: When Will Clinical Laboratories See the Revolution?” September 9, 2016.)

Now, researchers have demonstrated that even biomarkers within human skin can be tested by medical wearable devices. “Lab-on-skin” has entered the pathology vernacular.

Lab-on-Skin Constantly Measures Physiological Data

According to ACS Nano, lab-on-skin devices are small electronic patches worn directly on the skin that noninvasively measure a variety of physiological data. These flexible gadgets can interpret information including:

  • body temperature;
  • blood oxygenation;
  • hydration;
  • blood pressure;
  • glucose;
  • potassium;
  • sodium; and,
  • lactate and pH levels in individuals.

The devices may also be used for wound care, prosthetics and rehabilitation, as well as for optogenetics and human-machine interfaces (HMI).

The image above from the ACS Nano article demonstrates various lab-on-skin devices, including: an NFC tattoo with a bare die chip mounted on an acrylic adhesive film; a soft radio sensor with commercial chips encapsulated in a fluid/ecoflex package; and, a sweat sensor on silicone foam. Each of these devices could be capable of delivering actionable diagnostic data to anatomic pathologists and clinical laboratories. (Image copyright: ACS Nano.)

Lab-on-skin technology can be utilized to read electrophysiological signals typically measured by electrodes placed on various parts of the body, such as:

The direct connection between the patches and the skin allows for continuous and precise data collection without the threat of drying out that comes with traditional electrodes.

Nanotechnology Driving Clinical Laboratory Diagnostic Applications

Because it is the largest organ in the body, skin provides a perfect pathway to convey biological information originating from various parts of the body, such as inner organs, muscles, blood vessels, and the dermis and epidermis.

The ACS Nano article discusses advancements in the designs and materials used for lab-on-skin patches. In addition to the term “lab-on-skin,” these devices may also be referred to as electronic skin, epidermal electronics, and electronic tattoos. They have untapped potential in a variety of clinical applications, including:

For example, researchers at the University of Illinois at Urbana-Champaign have created an epidermal nanotechnology device that utilizes sensors and wireless interfaces to measure ultraviolet (UV) exposure, a risk factor for skin cancers.

“Our goal with this research is to establish a set of foundational materials and device designs for systems that can improve health outcomes by providing information on UV exposure,” John A. Rogers, PhD, and Professor of Materials Science and Engineering and Professor of Chemistry told Nanowerk Spotlight.

Nanotechnology employs extremely small particles performed at the nanoscale (about 1 to 100 nanometers). This field is emerging as a vital element behind cutting-edge innovations in medicine and healthcare.

“We developed new chemistries that yield color changes that quantitatively relate to total exposure dose, separately in both the UV-A and UV-B regions of the solar spectrum,” explained Rogers. “Our formulations have the additional advantage that they provide soft, low modulus mechanics to enhance comfort and biocompatibility with the skin surface.”

Mini-Laboratory Devices Could Push Pathology Data to Clinical Laboratories

The combination of using lab-on-skin devices with nanotechnology can provide researchers and medical professionals a multifunctional and valuable tool for health monitoring and the diagnosis of diseases. However, more research and clinical studies are needed to establish the validity of using lab-on-skin devices in healthcare applications.

Nevertheless, clinical laboratories and pathology groups will be handling more data in the future, generated by these miniature laboratory devices. Their usefulness, especially in challenging healthcare environments, is only beginning to be fully discovered.

—JP Schlingman

Related Information:

A Lab-on-Skin: A Review of Flexible and Stretchable Electronics for Wearable Health Monitoring (downloadable PDF)

Lab-on-Skin: A Review of Flexible and Stretchable Electronics for Wearable Health Monitoring (original ACS Nano article)

Lab-on-Skin: Nanotechnology Electronics for Wearable Health Monitoring

Stick-on Epidermal Electronics Tattoo to Measure UV Exposure

Nanotechnology in Healthcare (Part 1: Fitness Monitoring, Diagnostics and Prevention)

Nanotechnology in Healthcare (Part 2: Nanomedicine Therapy)

Breathable, Wearable Electronics on Skin for Long-term Health Monitoring

Nano-chip Promises to Heal Organs at a Touch

IBM and Mount Sinai Researchers Develop Innovative Medical Lab-on-a-Chip Solution

Lab-on-a-Chip Diagnostics: When Will Clinical Laboratories See the Revolution?

Researchers at University of Rhode Island Unveil Lab-on-Paper Test Capable of Multireagent Diagnostics: Could Enable ‘Diagnostics Without the Lab’ Say Developers

Sleek ‘Lab in a Needle’ Is an All-in-One Device That Detects Liver Toxicity in Minutes during a Study, Showing Potential to Supplant Some Medical Laboratory Tests


New Optomechanical Fluidic Sensor Analyzes Cell Mechanics in the Human Body and May Provide Clinical Laboratories with Useful New Diagnostic Tool

Researchers believe newly developed optomechanical technology might eventually be used by medical laboratories

Pathologists and medical laboratory scientists have long been aware of the parallel between cancer and the mechanical properties located in cells. However, a diagnostic tool to assess these properties has until now been unavailable. This may soon change.

A team at the University of Illinois at Urbana-Champaign (UIUC) recently created a technique involving “OptoMechanoFluidics” that might increase understanding of how diseases reshape the mechanical attributes of cells in the human body. The researchers’ innovative opto-mechano-fluidic approach could provide a new way to study how human cells congregate in tissue and bones by examining high-speed photonic sensing of free-flowing particles in the body at rates potentially reaching 10,000 particles per second.

The researchers published their findings in Optica, the online journal of the Optical Society (OSA). Gaurav Bahl, PhD, Assistant Professor, Mechanical Science and Engineering at UIUC, was one of the authors of the study. (See Optica, “High-throughput sensing of freely flowing particles with optomechanofluidics,” Vol. 3, Issue 6, pp. 585-591, 2016.) (more…)

New Approach to Detecting Circulating Tumor Cells in Blood Uses Acoustic Sound Waves and Researchers Are Hopeful that the Technology Can Lead to a Medical Laboratory Test

Innovative device uses acoustic sound waves to gently separate circulating cancer cells from white blood cells

In many respects, the ability to separate and identify circulating tumor cells (CTCs) is one of the holy grails of cancer diagnostics. It is widely believed that a clinical laboratory test that can effectively identify CTCs would contribute to earlier detection of cancer and improved outcomes for caner patients.

Pathologists will be interested to learn about a useful new tool that can flag circulating tumor cells. Researchers say that this approach enables them to determine if a cancerous tumor is going to spread, without tagging tumor cells with harsh chemicals. This gentler alternative to current diagnostic methods involves an innovative device that uses “tilted” sound waves to sort tumor cells from white blood cells, noted a report in Headlines & Global News.

This device is about the size of a cell phone. It was developed by a team of scientists from the Pennsylvania State University (PSU), Massachusetts Institute of Technology (MIT) and Carnegie Mellon University (CMU).

Their research was funded by the National Institutes of Health (NIH) and the National Science Foundation (NSF). The research study was published by PNAS, the journal of the U.S. National Academy of Sciences, January 5, 2015. (more…)