Proteins in human saliva make up its proteome and may be the key to new, precision medicine diagnostics that would give clinical pathologists new capabilities to identify disease
Clinical pathologists may soon have an array of new precision medicine diagnostic tools based on peoples’ saliva. There are an increasing number of “–omes” that can be the source of useful diagnostic biomarkers for developing clinical laboratory tests. The latest is the world’s first saliva protein biome wiki.
Called the Human Salivary Proteome Wiki (HSP Wiki), the “public data platform,” which was created by researchers at the University of Buffalo, is the “first of its kind,” according to Labroots, and “contains data on the many thousands of proteins present in saliva.”
The HSP Wiki brings together data from independent studies on proteins present in human saliva. One of the researchers’ goals is to speed up the development of saliva-based diagnostics and personalized medicine tools.
In “The Human Salivary Proteome Wiki: A Community-Driven Research Platform,” published in the Journal of Dental Research, the researchers wrote, “Saliva has become an attractive body fluid for on-site, remote, and real-time monitoring of oral and systemic health. At the same time, the scientific community needs a saliva-centered information platform that keeps pace with the rapid accumulation of new data and knowledge by annotating, refining, and updating the salivary proteome catalog.
“We developed the Human Salivary Proteome (HSP) Wiki as a public data platform for researching and retrieving custom-curated data and knowledge on the saliva proteome. … The HSP Wiki will pave the way for harnessing the full potential of the salivary proteome for diagnosis, risk prediction, therapy of oral and systemic diseases, and preparedness for emerging infectious diseases,” they concluded.
“This community-based data and knowledge base will pave the way to harness the full potential of the salivary proteome for diagnosis, risk prediction, and therapy for oral and systemic diseases, and increase preparedness for future emerging diseases and pandemics,” Stefan Ruhl, DDS, PhD (above right, with Omer Gokcumen, PhD, Associate Professor of Biological Sciences on left), Professor, Department of Oral Biology, University of Buffalo, and lead researcher of the study, told Labroots. Development of precision medicine clinical laboratory diagnostics is part of their research goals. (Photo copyright: University of Buffalo.)
Where Does Saliva Come From?
Saliva is a complex biological fluid that has long been linked to oral health and the health of the upper gastrointestinal tract. Only recently, though, have scientists begun to understand from where in the body saliva proteins originate.
The authors wrote: “Salivary proteins are essential for maintaining health in the oral cavity and proximal digestive tract, and they serve as potential diagnostic markers for monitoring human health and disease. However, their precise organ origins remain unclear.
“Through transcriptomic analysis of major adult and fetal salivary glands and integration with the saliva proteome, the blood plasma proteome, and transcriptomes of 28+ organs, we link human saliva proteins to their source, identify salivary-gland-specific genes, and uncover fetal- and adult-specific gene repertoires,” they added.
“Our results pave the way for future investigations into glandular biology and pathology, as well as saliva’s use as a diagnostic fluid,” the researchers concluded.
Saliva plays a crucial role in digestion by breaking down starches. It also provides a protective barrier in the mouth. When salivary glands malfunction, patients can face serious health consequences. Although clinicians and scientists have long understood the importance of saliva to good health, the question now is whether it contains markers of specific diseases.
“The Human Salivary Proteome Wiki contains proteomic, genomic, transcriptomic data, as well as data on the glycome, sugar molecules present on salivary glycoproteins. New data goes through an interdisciplinary team of curators, which ensures that all input data is accurate and scientifically sound,” noted Labroots.
The graphic above “shows the interconnectedness of the thousands of salivary proteins originating from blood plasma, parotid glands, and submandibular and sublingual glands. The diagram is one of many tools available to researchers and clinicians through the Human Salivary Proteome Wiki,” noted a UBNow blog post. (Graphic copyright: University of Buffalo.)
Omics and Their Role in Clinical Laboratory Diagnostics
Proteomics is just one of several hotly-researched -omics that hold the potential to develop into important personalized medicine and diagnostics tools for pathologists. Genomics is a related area of research being studied for its potential to benefit precision medicine diagnostics.
However, unlike genomes, which do not change, proteomes change constantly. That is one of the main reasons studying the human salivary proteome could lead to valuable diagnostics tools.
Combining the study of the -omes with tools like mass spectrometry, a new era of pathology may be evolving. “With the rapid decrease in the costs of omics technologies over the past few years, whole-proteome profiling from tissue slides has become more accessible to diagnostic labs as a means of characterization of global protein expression patterns to evaluate the pathophysiology of diseases,” noted Pathology News.
Saliva and the Age of Precision Medicine
The study of the -omes may be an important element in the evolution of precision medicine, because of its ability to provide information about what is happening in patients’ bodies at the point of care.
Thus, a full understanding of the proteome of saliva and what causes it to change in response to different health conditions and diseases could open the door to an entirely new branch of diagnostics and laboratory medicine. It is easy and non-invasive to gather and, given that saliva contains so much information, it offers an avenue of study that may improve patients’ lives.
It also would bring us closer to the age of precision medicine where clinical laboratory scientists and pathologists can contribute even more value to referring physicians and their patients.
Pathologists can be paid for their role in identifying and recruiting patients for basket studies and reporting results of medical laboratory tests
Anatomic
pathologists who biopsy, report, and diagnosis cancer will benefit from a
better understanding of basket
studies and their application in developing cancer treatment therapies. Such
studies can lead to more documentation of the effectiveness of various therapies
for cancers with specific gene
signatures.
The US
National Library of Clinical Medicine defines basket studies as “a new sort
of clinical studies to identify patients with the same kind of mutations and
treat them with the same drug, irrespective of their specific cancer type. In
basket studies, depending on the mutation types, patients are classified into ‘baskets.’
Targeted therapies that block that mutation are then identified and assigned to
baskets where patients are treated accordingly.”
“Historically, cancer clinical trials have been centered on the treatment of cancer based on the anatomic location in the body, like breast cancer or brain cancer or lung cancer. A basket study is a novel trial design that includes patients with a certain molecular aberration regardless of location or tissue of origin of cancer in the body. The genomic revolution in oncology has fueled these studies,” Vivek Subbiah, MD, Associate Professor and Medical Director, Clinical Center for Targeted Therapy ( Phase 1 trials program), at the University of Texas MD Anderson Cancer Center in Houston, told Cancer Therapy Advisor. (Photo copyright: MD Anderson Cancer Center.)
Basket Studies Get Results
During a basket study, researchers may find that a drug’s
effectiveness at targeting “a genetic mutation at one site can also treat the
same genetic mutation in cancer in another area of the body,” noted Pharmacy
Times, which also pointed out basket studies are often starting points for
larger oncology trials about drugs.
For example, it was a basket study which found that vemurafenib (marketed as
Zelboraf), intended for treatment of V600E, a mutation of the BRAF gene, may also treat Erdheim-Chester
disease (a rare blood disorder) in patients who have the BRAF V600 gene
mutation, Pharmacy Times reported.
Additionally, the US Food and Drug Administration’s approval
of the cancer drug Vitrakvi (larotrectinib), an oral TRK
inhibitor, marked the first treatment to receive a “tumor-agnostic
indication at time of initial FDA approval,” a Bayer
news release stated. The drug’s efficacy, Pharmacy Times noted, was
found in a “pivotal” basket study.
Basket Studies, a Master Protocol Trial Design
The basket study technique is an example of a master protocol trial design. The FDA defines a master protocol as “a protocol designed with multiple substudies, which may have different objectives and involves coordinated efforts to evaluate one or more investigational drugs in one or more disease subtypes within the overall trial structure. A master protocol may be used to conduct the trial(s) for exploratory purposes or to support a marketing application and can be structured to evaluate, in parallel, different drugs compared to their respective controls or to a single common control.”
Other master protocols include umbrella studies and platform
studies, according to Cancer Therapy Advisor, which noted that each
master protocol trial design has its own unique objectives:
Umbrella studies look at the effectiveness of
multiple drugs on one type of cancer;
Platform trials investigate the effectiveness of
multiple therapies on one disease on an ongoing basis; and
Basket studies focus on the effectiveness of one
therapy on patients with different cancers based on a biomarker.
“In contrast to traditional trials designs, where a single
drug is tested in a single disease population in one clinical trial, master
protocols use a single infrastructure, trial design, and protocol to
simultaneously evaluate multiple drugs and or disease populations in multiple
substudies, allowing for efficient and accelerated drug development,” states
the FDA draft guidance, “Master
Protocols: Efficient Clinical Trial Design Strategies to Expedite Development
of Oncology Drugs and Biologics.”
Final FDA guidance on master protocols design is expected early in 2020, an FDA spokesperson told Cancer Therapy Advisor.
While master protocol studies show promise, they generally
have small sample sizes, noted researchers of a study published in the journal Trials.
And some researchers have ethical concerns about basket studies.
Nevertheless, basket studies appear to hold promise for precision medicine.
Anatomic pathologists may want to follow some of them or find a way to get
involved through identifying clinical laboratory tests and reporting the results.
Using animal blood, the researchers hope to improve the accuracy of AI driven diagnostic technology
What does a cheetah, a tortoise, and a Humboldt penguin have
in common? They are zoo animals helping scientists at Saarland University in
Saarbrücken, Germany, find biomarkers that can help computer-assisted diagnoses
of diseases in humans at early stages. And they are not the only animals
lending a paw or claw.
In their initial research, the scientists used blood samples
that had been collected during routine examinations of 21 zoo animals between
2016 and 2018, said a news
release. The team of bioinformatics
and human genetics experts
worked with German zoos Saarbrücken and Neunkircher for the study. The project
progresses, and thus far, they’ve studied the blood of 40 zoo animals, the
release states.
This research work may eventually add useful biomarkers and
assays that clinical
laboratories can use to support physicians as they diagnose patients,
select appropriate therapies, and monitor the progress of their patients. As medical
laboratory scientists know, for many decades, the animal kingdom has been
the source of useful insights and biological materials that have been
incorporated into laboratory assays.
“Measuring the molecular blood profiles of animals has never
been done before this way,” said Andreas
Keller, PhD, Saarland University Bioinformatics Professor and Chair for
Clinical Bioinformatics, in the news release. The Saarland researchers published
their findings in Nucleic Acids
Research, an Oxford
Academic journal.
“Studies on sncRNAs [small non-coding RNAs] are often largely based on homology-based information, relying on genomic sequence similarity and excluding actual expression data. To obtain information on sncRNA expression (including miRNAs, snoRNAs, YRNAs and tRNAs), we performed low-input-volume next-generation sequencing of 500 pg of RNA from 21 animals at two German zoological gardens,” the article states.
Can Animals Improve the Accuracy of AI to Detect Disease
in Humans?
However, the researchers perceived an inability for AI and machine learning to
discern real biomarker patterns from those that just seemed to fit.
“The machine learning methods recognize the typical
patterns, for example for a lung tumor or Alzheimer’s disease. However, it is
difficult for artificial intelligence to learn which biomarker patterns are
real and which only seem to fit the respective clinical picture. This is where
the blood samples of the animals come into play,” Keller states in the news
release.
“If a biomarker is evolutionarily conserved, i.e. also
occurs in other species in similar form and function, it is much more likely
that it is a resilient biomarker,” Keller explained. “The new findings are now
being incorporated into our computer models and will help us to identify the
correct biomarkers even more precisely in the future.”
Andreas Keller, PhD (left), and zoo director Richard Francke (right), hold a pair of radiated tortoises that participated in the Saarland University study. (Photo copyright: Oliver Dietze/Saarland University.)
“Because blood can be obtained in a standardized manner and
miRNA expression patterns are technically very stable, it is easy to accurately
compare expression between different animal species. In particular, dried blood
spots or microsampling devices appear to be well suited as containers for
miRNAs,” the researchers wrote in Nucleic Acids Research.
Animal species that participated in the study include:
Additionally, human volunteers contributed blood specimens
for a total of 19 species studied. The scientists reported success in capturing
data from all of the species. They are integrating the information into their
computer models and have developed a public database of their
findings for future research.
“With our study, we provide a large collection of small RNA
NGS expression data of species that have not been analyzed before in great
detail. We created a comprehensive publicly available online resource for
researchers in the field to facilitate the assessment of evolutionarily
conserved small RNA sequences,” the researchers wrote in their paper.
Clinical Laboratory Research and Zoos: A Future
Partnership?
This novel involvement of zoo animals in research aimed at improving
the ability of AI driven diagnostics to isolate and identify human disease is
notable and worth watching. It is obviously pioneering work and needs much
additional research. At the same time, these findings give evidence that there
is useful information to be extracted from a wide range of unlikely sources—in
this case, zoo animals.
Also, the use of artificial intelligence to search for
useful patterns in the data is a notable part of what these researchers
discovered. It is also notable that this research is focused on sequencing DNA
and RNA of the animals involved with the goal of identifying sequences that are
common across several species, thus demonstrating the common, important
functions they serve.
In coming years, those clinical laboratories doing genetic
testing in support of patient care may be incorporating some of this research
group’s findings into their interpretation of certain gene sequences.
Ever shrinking “lab-on-a-…” technologies, a boon to medical laboratories and anatomic pathologists in remote resource-strapped regions, also have a place in modern labs
Researchers took another leap forward in reducing the size of clinical laboratory diagnostic tests and observational tools. This demonstration involved lab-on-a-fiber technology and showed promise in both monitoring anatomic pathology biomarkers in vivo and supplementing the abilities of existing lab-on-a-chip and microfluidic devices.
In 2013, Dark Daily reported on research into an implantable laboratory-on-a-chip (LOC) for monitoring blood chemistry during chemotherapy. It was a major breakthrough at the time, which promised new and powerful tools for cancer treatment regimens.
However, most LOC systems aren’t designed for wet environments. Also, while microfluidics and flexible membranes allow for smaller footprints and tighter placement, they are still invasive in ways that might make patients uncomfortable or make real-world use less than ideal. And, long-term use brings further complications, such as corrosion or foreign-body granulomas.
Thus, lab-on-a-fiber’s ability to function in vivo, is one of the device’s principal advantages, as ExtremeTech noted.
Lab-on-a-fiber technology addresses many concerns. It is small enough to insert directly into organs, muscle mass, or veins when used as biosensors. And the fibers can return a wealth of information by using light and reflection, while allowing for minimal discomfort and precision placement.
Schematic of the lab-on-a-fiber biosensing principle. A metallic nanostructure supporting a resonant plasmonic mode is integrated on the optical fiber tip. When a molecular binding event occurs at the sensor surface, the reflectance peak associated to the plasmonic mode shifts towards longer wavelengths. (Image and caption copyright: Analyst/The Royal Society of Chemistry.)
The Past and Future of Scaling Clinical Laboratory Testing
Developers believe lab-on-a-fiber approaches could offer further adaptability and functionality to other “lab-on-a-…” technologies. For example, as highlighted in Advanced Science News, researchers are employing lab-on-a-fiber technologies to further refine and improve LOC functions and designs.
“As the scientific world moves inexorably to smaller dimensions … The emerging concept of ‘lab‐on‐fiber’ will give the optical fiber platform additional (highly integrated) functionalities,” noted Deepak Uttamchandani, PhD, Vice Dean Research, Faculty of Engineering, and, Robert Blue, PhD, Research Fellow, both at the University of Strathclyde, Glasgow, UK, in their review paper, “Recent Advances In Optical Fiber Devices for Microfluidics Integration.” The paper, published in the Journal of Biophotonics, examined “the recent emergence of miniaturized optical fiber-based sensing and actuating devices that have been successfully integrated into fluidic microchannels that are part of microfluidic and lab‐on‐chip systems.”
In his review paper on the emerging concept of lab-on-a-fiber, Deepak Uttamchandani, PhD, notes, “The versatility of the optical fiber platform has already allowed researchers to conduct immunoassays in microchannels using both fluorescently‐labelled and label‐free formats whilst gaining advantages of reduced assay time and increased sensitivity.” (Photo copyright: University of Strathclyde.)
Lab-on-a-Fiber: Another Step Forward or a Major Change?
At each milestone in the scaling of clinical laboratory testing, experts and media outlets predicted the demise of big laboratories and the dawn of a POC-centric testing era. Yet, despite 20-plus years of progress, this has yet to happen.
While it is critical for anatomical pathology leaders and clinical laboratory managers to stay abreast of developments in testing technology, much of the innovation behind lab-on-a-fiber remains strictly in the research realm. Challenges to the commercialization of these new techniques include both physical factors, such as design and manufacture of ready-to-use tests, and regulatory concerns, including FDA clearances and payer approval of new assays and diagnostic procedures.
Until researchers and test manufacturers overcome these hurdles, threats to current standards and workflows are minimal. However, much like the gains in scale realized through incorporating lab-on-a-chip concepts into clinical laboratory testing, the research powering these innovations might prove useful in further improving and expanding medical laboratory testing options.
Mobile point-of-care (POC) smartphone-based nucleic acid assay allows for quick turn arounds and accurate information in any healthcare setting, including resource limited and remote environments
Clinical laboratory equipment is becoming more effective even as it shrinks in size and cost. One such device has been developed by Ozcan Laboratory Group, headed by UCLA professor Aydogan Ozcan, PhD. It is a portable, smartphone-based mobile lab with sensitivity and reliability on par with large-scale medical laboratory-based equipment.
Ozcan Lab’s portable DNA detection system, according to a UCLA press release, “leverages the sensors and optics of cellphones” and adapts them to read and report the presence of DNA molecules. The sensor uses a new detector dye mixture and reportedly produces a signal that is 10 to 20 times brighter than previous detector dye outputs.
Nucleic acid detecting assays are crucial tools anatomic pathologists use to identify pathogens, detect residual disease markers, and identify treatable mutations of diseases. Due to the need for amplification of nucleic acids for detection with benchtop equipment, there are challenges associated with providing rapid diagnostics outside the clinical laboratory.
The device developed by Ozcan Labs (above) is a “field-portable and cost-effective mobile-phone-based nucleic acid amplification and readout platform [that] is broadly applicable to other real-time nucleic acid amplification tests by similarly modulating intercalating dye performance. It is compatible with any fluorescence-based assay that can be run in a 96-well microplate format, making it especially valuable for POC and resource-limited settings.” (Caption and photo copyright: American Chemical Society.)
Using the new mobile POC nucleic acid testing system developed by Ozcan et al, pathologists can effectively step away from the lab to perform rapid POC testing and accelerated diagnostics onsite, rather than needing to transport materials to and from a central laboratory. The mobile testing assay enables pathologists to carry a medical laboratory with them into the field, or into limited-resource or decentralized testing environments, without sacrificing quality or sensitivity. And according to the ACS Nano article, at a relatively low-cost compared to benchtop nucleic acid testing equipment.
In an article published in Future Medicine, Ozcan and Hatice Ceylan Koydemir, PhD, a post-doctoral researcher in electrical engineering at UCLA, comment on the growing interest in mobile POC diagnostics, stating that smartphone-based devices and platforms have the potential “to be used for early detection and prevention of a variety of health problems.”
According to the article, smartphone-based sensing and imaging platforms have been developed to:
Smartphones, according to Ozcan and Koydemir, have been adapted to a range of biomedical measurement tools, “have the potential to transform traditional uses of imaging, sensing, and diagnostic systems, especially for point-of-care applications and field settings,” and can provide speedy results.
A ‘Highly Stable’ and Sensitive System
The proof-of-concept study of Ozcan Lab’s new smartphone-based detection system and new detector dye mixture was led by Janay E. Kong, PhD in bioengineering at UCLA, with the help of Ozcan and fellow professors Dino Di Carlo, PhD, professor of bioengineering and mechanical and aerospace engineering at UCLA, and Omai Garner, PhD, associate professor of clinical microbiology at the David Geffen School of Medicine at UCLA.
According to an article in Bioscience Technologies, the new smartphone DNA detection system addresses issues with detection of light emitted from intercalator dyes, which are normally “too subtle and unstable for regular cellphone camera sensors.” The new system uses loop-mediated isothermal amplification (LAMP) to amplify DNA in connection with a newly developed dye that uses hydroxynaphthol blue (HNB) as an indicator.
The inclusion of HNB into the dye, according to the original research study, “yields 20 times higher fluorescent signal change over background compared to current intercalating dyes,” making the results bright enough for smartphone camera sensors without “interfering with the nucleic acid amplification process.” The original study reports that the digital LAMP system and use of the HNB intercalating dye, in fact, provided “significantly enhanced performance compared to a benchtop reader with standard LAMP conditions.”
Ozcan labs shows no signs of slowing down their development of mobile POC diagnostic devices. The development of these smartphone-based tools may provide unique and much-needed equipment for clinical pathologists given the rising interest in mobile healthcare worldwide.
