Findings could reduce the need for self-reporting in future nutritional studies and lead to new clinical laboratory testing
Clinical laboratory testing may one day influence whether a person snacks on a bag of chips every day or chooses to eat healthy foods instead.
Researchers at the National Institutes of Health (NIH) reported that they have identified biomarkers in blood and urine that can indicate an individual’s consumption of ultra-processed foods (UPF).
Scientists discovered a signature that is predictive of a dietary pattern that’s high in ultra-processed food, study leader Erikka Loftfield, PhD, MPH, epidemiologist and principal investigator with the NIH, told the Associated Press (AP).
Using data on the biomarkers—metabolites left after the body breaks down food—the researchers devised a “poly-metabolite score” that could potentially “reduce the reliance on, or complement the use of, self-reported dietary data in large population studies,” according to an NIH press release.
This will be helpful because, according to the AP, “Typical nutrition studies rely on recall: asking people what they ate during a certain period. But such reports are notoriously unreliable because people don’t remember everything they ate, or they record it inaccurately.”
“Limitations of self-reported diet are well known. Metabolomics provides an exciting opportunity to not only improve our methods for objectively measuring complex exposures like diet and intake of ultra-processed foods, but also to understand the mechanisms by which diet might be impacting health,” said Loftfield in the press release.
Thus, it’s conceivable that one day clinical laboratory testing could affect people’s food choices and help to improve their health.
“There’s a need for both a more objective measure and potentially also a more accurate measure,” Erikka Loftfield, PhD, MPH, epidemiologist and principal investigator with the NIH, told the Associated Press. (Photo copyright: National Cancer Institute.)
Study Methodology
The findings were based in part on an earlier study of 718 AARP members, aged 50-74, who agreed to submit blood and urine samples. The participants also completed dietary recall reports.
“The researchers found hundreds of metabolites that correlated with the percentage of energy from ultra-processed foods in the diet,” the NIH press release noted. “Using machine learning, researchers identified metabolic patterns associated with high intake of ultra-processed foods and calculated poly-metabolite scores for blood and urine separately.”
To test their findings, the researchers referred to a 2019 NIH study involving 20 adults aged 18 to 50. Under carefully controlled conditions, these participants spent two weeks consuming high levels of ultra-processed foods, followed by two weeks consuming no ultra-processed foods. As with the AARP cohort, they also submitted blood and urine samples. The poly-metabolite score proved to be an accurate measure of which diets they had consumed, the researchers reported.
The researchers acknowledged limitations in the study that will necessitate further research. “Study participants were older US adults whose diets may vary from other populations,” the authors noted. “Poly-metabolite scores should be evaluated and iteratively improved in populations with diverse diets and a wide range of UPF intake.”
Ultra-Processed Foods Defined
The NIH defines ultra-processed foods as “ready-to-eat or ready-to-heat, industrially manufactured products, typically high in calories and low in essential nutrients.” Diets high in these foods have been associated with “increased risk of obesity and related chronic diseases, including some types of cancer,” the press release noted.
In identifying these foods, the researchers cited a 2019 paper published in the journal Public Health Nutrition (PHN). The paper relied on the NOVA classification system, which makes a distinction between “processed” and “ultra-processed” foods. The latter typically contain “food substances never or rarely used in kitchens,” or cosmetic additives “whose function is to make the final product palatable or more appealing,” the PHN paper noted.
“From sugary cereals at breakfast to frozen pizzas at dinner, plus in-between snacks of potato chips, sodas and ice cream, ultra-processed foods make up about 60% of the US diet,” the AP reported in an earlier story. “For kids and teens, it’s even higher—about two-thirds of what they eat.”
Research could lead to new biomarkers for clinical laboratory tests that spot disease early in patients
As we have covered in previous Dark Daily ebriefs, there are ongoing efforts to develop diagnostic assays that use human breath as the specimen. One early example was the breath specimen for Helicobacter pylori (H. pylori) testing—the bacteria that causes peptic ulcers—in the 1990s. Thus, a new sensor developed by scientists at Zhejiang University in China that can detect the presence of lung cancer in human breath will be of interest to medical laboratory scientists and clinical laboratories working on such testing.
In a proof-of-concept study, the Zhejiang University researchers “developed ultrasensitive nanoscale sensors that in small-scale tests distinguished a key change in the chemistry of the breath of people with lung cancer,” according to an American Chemical Society (ACS) news release.
The new research exemplifies how instruments are becoming increasingly sensitive to detection of smaller specimen quantities, making it possible to even use exhaled breath to diagnose lung cancer, noted a review article published in Science Direct.
“This study presents a novel Pt@InNiOx [platinum (Pt), indium (In), nickel (Ni)] nanoflake isoprene sensor that achieves an exceptionally low limit of detection at two parts per billion (2ppb)—the lowest reported for isoprene sensor to date,” wrote study lead author, Pingwei Liu, PhD (above), distinguished research fellow, Zhejiang University, et al, in ACS Sensors. “Our work not only provides a breakthrough in low-cost, noninvasive cancer screening through breath analysis but also advances the rational design of cutting-edge gas sensing materials.” Clinical laboratories working with breath sample biomarkers will be intrigued by this new advancement in the technology. (Photo copyright: Zhejiang University.)
Finding the Breakthrough Sensor
The Zhejiang University researchers were motivated by the potential for rapid gas sensing in diagnostics. Many gases, including carbon dioxide, are exhaled. But one particular gas, isoprene, they found “can indicate the presence of lung cancer,” the news release states.
However, while breath is readily available, it is not easy to isolate breath biomarkers. That is because a detector needs to “differentiate between volatile chemicals, withstand the natural humidity of exhaled breath, and detect tiny quantities of specific chemicals,” New Atlas explained.
To detect small specimen quantities of isoprene, a highly sensitive sensor needed to be developed—one that would be a step up from standard indium oxide-based breath sensors.
The scientists experimented with a series of indium (III) oxide (In203)-based nanoflake sensors until they found the sensor that performed consistently in nine experiments. They called it Pt@InNiOx for the platinum (Pt), indium (In), and nickel (Ni) it contained.
According to the news release, the Pt@InNiOx sensor:
Had “sensitivity that far surpassed earlier sensors” as evidenced by detection of isoprene as low as 2ppb.
Emphasized isoprene attraction over other volatile compounds in breath.
Has advanced sensitivity due to “Pt nanoclusters uniformly anchored on the nanoflakes” activating the isoprene sensing.
Gadget Review described the innovation as a “significant advance in diagnostic capability” that uses nanoscale technology along with “indium oxide nanoflakes with platinum-based nanoclusters.”
Developing the Lung Cancer Diagnostic Device
The scientists put their Pt@InNiOx nanoflakes into a portable sensing device for breath analysis. They then inserted breath samples from 13 people including five who had lung cancer. They found that:
In samples from people with cancer, the device enabled detection of isoprene levels lower than 40 ppb.
In samples from cancer-free participants, the device found isoprene levels more than 60 ppb.
“We integrate these ultrasensitive Pt@InNiOx nanoflakes into a miniaturized portable electronic device that successfully distinguishes lung cancer patients with expiratory isoprene below 40ppb, from the healthy population with isoprene above 60 ppb, enabling an accurate diagnosis in clinics,” wrote study lead author, Pingwei Liu, PhD, distinguished research fellow, Zhejiang University, et al, in ACS Sensors.
“As the isoprene hits the nanoflakes, electron release is sparked in a way that can be measured,” MSN Health reported, adding that the nanoflakes were also able to find isoprene in other chemicals and operate even in humid conditions.
Breath as Lab Test Biomarker for Cancer
In the United States, more people die from lung cancer than any other form of cancer, according to US Centers for Disease Control and Prevention statistics. The CDC data show there were 209,500 new lung and bronchus cancer cases in 2022, the most recent year for available data.
The Zhejiang University scientists reportedly plan to continue their research on the sensing materials and link between isoprene and lung cancer.
Studies continue to show many components in human breath can be used as clinical laboratory test biomarkers. Assays that use the breath as specimen may one day play an important role in early diagnosis of lung cancer and other diseases.
Study findings could lead to new clinical laboratory screening tests that determine risk for cancer
New disease biomarkers generally lead to new clinical laboratory tests. Such may be the case in an investigational study conducted at the University of Oxford in the United Kingdom (UK). Researchers in the university’s Cancer Epidemiology Unit (CEU) have discovered certain proteins that appear to indicate the presence of cancer years before the disease is diagnosed.
The Oxford scientists “investigated associations between 1,463 plasma proteins and 19 cancers, using observational and genetic approaches in participants of the UK Biobank. They found 618 protein-cancer associations and 317 cancer biomarkers, which included 107 cases detected over seven years before the diagnosis of cancer,” News Medical reported.
To conduct their study, the scientists turned to “new multiplex proteomics techniques” that “allow for simultaneous assessment of proteins at a high-scale, especially those that remain unexplored in the cancer risk context,” News Medical added.
Many of these proteins were in “blood samples of people who developed cancer more than seven years before they received a diagnosis,” an Oxford Population Health news release notes.
“To be able to prevent cancer, we need to understand the factors driving the earliest stages of its development. These studies are important because they provide many new clues about the causes and biology of multiple cancers, including insights into what’s happening years before a cancer is diagnosed,” said Ruth Travis, BA, MSc, DPhil, senior molecular epidemiologist at Oxford Population Health and senior study author, in the news release.
“We now have technology that can look at thousands of proteins across thousands of cancer cases, identifying which proteins have a role in the development of specific cancers and which may have effects that are common to multiple cancer types,” said Ruth Travis, BA, MSc, DPhil (above), senior molecular epidemiologist, Oxford Population Health, in a news release. The study findings could lead to new clinical laboratory screening tests for cancer. (Photo copyright: University of Oxford.)
Proteomics to Address Multiple Cancers Analysis
In their published paper, the Oxford scientists acknowledged other research that identified links between blood proteins and risk for various cancers, including breast, colorectal, and prostate cancers. They saw an opportunity to use multiplex proteomics methods for the simultaneous measurement of proteins “many of which have not previously been assessed for their associations with risk across multiple cancer sites,” the researchers noted.
The researchers described “an integrated multi-omics approach” and the use of the Olink Proximity Extension Assay (PEA) to quantify 1,463 proteins in blood samples from 44,645 participants in the UK Biobank, a large biomedical database and resource to scientists.
Olink, a part of Thermo Fisher Scientific in Waltham, Mass., explains on its website that PEA technology “uniquely combines specificity and scalability to enable high-throughput, multiplex protein biomarker analysis.”
The researchers also compared proteins of people “who did and did not go on to be diagnosed with cancer” to determine differences and identify proteins that suggest cancer risk, News Medical reported.
Proteins Could Assist in Cancer Prevention
“To save more lives from cancer, we need to better understand what happens at the earliest stages of the disease. Data from thousands of people with cancer has revealed really exciting insights into how the proteins in our blood can affect our risk of cancer. Now we need to study these proteins in depth to see which ones could be reliably used for cancer prevention,” Keren Papier, PhD, senior nutritional epidemiologist at Oxford Population Health and joint lead author of the study, told News Medical.
While further studies and regulatory clearance are needed before the Oxford researchers’ approach to identifying cancer in its early stages can be used in patient care, their study highlights scientists’ growing interest in finding biomarker combinations that can predict or diagnose cancer even when it is presymptomatic. By focusing on proteins rather than DNA and RNA, researchers are turning to a source of information other than human genes.
For anatomic pathologists and clinical laboratory leaders, the Oxford study demonstrates how scientific teams are rapidly developing new knowledge about human biology and proteins that are likely to benefit patient care and diagnostics.
Small handheld device uses sound waves to detect certain clinical laboratory biomarkers in blood samples
University of Colorado Boulder researchers have developed a novel technology that uses sound waves to test for biomarkers in blood samples. In addition to being very easy to use, the handheld device is portable, highly sensitive, and delivers results in minutes. Though not ready for clinical use, this is yet another example of how researchers are developing faster diagnostic tests that can be performed in near-patient settings, and which do not have to be done in core laboratories, shortening time to answer.
The small instrument—referred to as an “acoustic pipette”—delivers sound waves to tiny particles within the device called “functional negative acoustic contrast particles” (fNACPs). These particles are cell-sized balls that can be customized with different coatings to identify specific biomarkers—such as viruses or proteins—in tiny blood samples, according to a news release.
To operate the device, the custom fNACPs are mixed with a drop of blood and then placed inside the acoustic pipette. The mixture is then blasted with sound waves, which forces particles carrying certain biomarkers to one side of the chamber where they are trapped while the rest of the blood is expelled. The captured biomarkers are then labeled with fluorescent tags and examined with lasers to determine how much of a specific biomarker is present.
“We’re basically using sound waves to manipulate particles to rapidly isolate them from a really small volume of fluid,” said Cooper Thome (above), PhD candidate in Chemical and Biological Engineering at UC Boulder and first author of the study in a news release. “It’s a whole new way of measuring blood biomarkers,” he added. Should further studies validate this approach, clinical laboratories may be able to use this technology to perform diagnostic tests with smaller volumes of patient samples. (Photo copyright: University of Colorado Boulder.)
Blood Testing Quickly and in Multiple Settings
To test their invention, the UC Boulder researchers examined antibodies against a protein called ovalbumin, which is found in egg whites and often used in the development of various vaccines. The scientists discovered that their device could detect the antibodies even in low amounts.
Current rapid tests known as lateral-flow assays can detect specific biomarkers in blood or urine samples but cannot determine how much of the biomarker is present. Enzyme-linked immunotherapy assays (ELISA), the leading clinical laboratory blood test, requires expensive equipment and can take hours to days for results to be received.
With UC Boulder’s new handheld device, tiny blood samples collected from a single finger prick could ensure accurate test results are available quickly at the point of care as well as outside of traditional healthcare settings. This would greatly benefit people in developing nations and underserved communities and may help ease test anxiety for individuals who are apprehensive about traditional blood tests.
“We’ve developed a technology that is very user friendly, can be deployed in various settings, and provides valuable diagnostic information in a short time frame,” said Wyatt Shields IV, PhD, Assistant Professor, Department of Chemical and Biological Engineering, UC Boulder, and senior author of the research in the news release.
“In our paper, we demonstrate that this pipette and particle system can offer the same sensitivity and specificity as a gold-standard clinical test can but within an instrument which radically simplifies workflows,” he added. “It gives us the potential to perform blood diagnostics right at the patient’s bedside.”
The graphic above, taken from UC Boulder’s published paper, illustrates how “fNACPs capture target biomarkers from whole blood samples. fNACPs are purified from blood components by acoustic trapping and captured biomarkers are labeled with a fluorescent antibody within the acoustic pipette. fNACP fluorescence is then measured to determine biomarker presence and concentration.” (Graphic/caption copyright: University of Colorado Boulder.)
Not Like Theranos
The authors of the UC Boulder study are cognizant of some skepticism surrounding the field of biosensing, especially after the downfall of Theranos. The scientists insist their technology is different and based on systematic experiments and peer-reviewed research.
“While what they (Theranos) claimed to do isn’t possible right now, a lot of researchers are hoping something similar will be possible one day,” said Thome in the news release. “This work could be a step toward that goal—but one that is backed by science that anybody can access.”
The device is still in its initial proof-of-concept stage, but the UC Boulder scientists have applied for patents for the apparatus and are searching for ways to scale its use and expand its capabilities.
“We think this has a lot of potential to address some of the longstanding challenges that have come from having to take a blood sample from a patient, haul it off to a lab, and wait to get results back,” Shields noted.
More research, studies, and regulatory reviews will be needed before this technology becomes available for regular, widespread use. But UC Boulder’s new blood testing device is another example of a research team using novel technology to test for known biomarkers in ways that could improve standard clinical laboratory testing.
Though not biomarkers per se, these scores for certain genetic traits may someday be used by clinical laboratories to identify individuals’ risk for specific diseases
Can polygenic risk scores (a number that denotes a person’s genetic predisposition for certain traits) do a better job at predicting the likelihood of developing specific diseases, perhaps even before the onset of symptoms? Researchers at the Broad Institute of MIT and Harvard (Broad Institute) believe so, and their study could have implications for clinical laboratories nationwide.
In cooperation with medical centers across the US, the scientists “optimized 10 polygenic scores for use in clinical research as part of a study on how to implement genetic risk prediction for patients,” according to a Broad Institute news release.
The research team “selected, optimized, and validated the tests for 10 common diseases [selected from a total of 23 conditions], including heart disease, breast cancer, and type 2 diabetes. They also calibrated the tests for use in people with non-European ancestries,” the news release notes.
As these markers for genetic risk become better understood they may work their way into clinical practice. This could mean clinical laboratories will have a role in sequencing patients’ DNA to provide physicians with information about the probability of a patient’s elevated genetic risk for certain conditions.
However, the effectiveness of polygenic risk scores has faced challenges among diverse populations, according to the news release, which also noted a need to appropriately guide clinicians in use of the scores.
“With this work, we’ve taken the first steps toward showing the potential strength and power of these scores across a diverse population,” said Niall Lennon, PhD (above), Chief Scientific Officer of Broad Clinical Labs. “We hope in the future this kind of information can be used in preventive medicine to help people take actions that lower their risk of disease.” Clinical laboratories may eventually be tasked with performing DNA sequencing to determine potential genetic risk for certain diseases. (Photo copyright: Broad Institute.)
Polygenic Scores Need to Reflect Diversity
“There have been a lot of ongoing conversations and debates about polygenic risk scores and their utility and applicability in the clinical setting,” said Niall Lennon, PhD, Chair and Chief Scientific Officer of Broad Clinical Labs and first author of the study, in the news release. However, he added, “It was important that we weren’t giving people results that they couldn’t do anything about.”
In the paper, Lennon and colleagues explained polygenic risk scores “aggregate the effects of many genetic risk variants” to identify a person’s genetic predisposition for a certain disease or phenotype.
“But their development and application to clinical care, particularly among ancestrally diverse individuals, present substantial challenges,” they noted. “Clinical use of polygenic risk scores may ultimately prevent disease or enable its detection at earlier, more treatable stages.”
The scientists set a research goal to “optimize polygenic risk scores for a diversity of people.”
While performing the polygenic risk score testing on participants, Broad Clinical Labs focused on 10 conditions—including cardiometabolic diseases and cancer—selected by the research team based on “polygenic risk score performance, medical actionability, and clinical utility,” the Nature Medicine paper explained.
For each condition, the researchers:
Identified “exact spots in the genome that they would analyze to calculate the risk score.”
Used information from the NIH’s All of Us Research Program to “create a model to calibrate a person’s polygenic risk score according to that individual’s genetic ancestry.”
The All of Us program, which aims to collect health information from one million US residents, has three times more people of non-European ancestry than other data sources developing genetic risk scores, HealthDay News reported.
20% of Study Participants Showed High Risk for Disease
To complete their studies, Broad Institute researchers processed a diverse group of eMERGE participants to determine their clinical polygenic risk scores for each of the 10 diseases between July 2022 and August 2023.
Listed below are all conditions studied, as well as the number of participants involved in each study and the number of people with scores indicating high risk of the disease, according to their published paper:
Over 500 people (about 20%) of the 2,500 participants, had high risk for at least one of the 10 targeted diseases, the study found.
Participants in the study self-reported their race/ancestry as follows, according to the paper:
White: 32.8%
Black: 32.8%
Hispanic: 25.4%
Asian: 5%
American Indian: 1.5%
Middle Eastern: 0.9%
No selection: 0.8%
“We can’t fix all biases in the risk scores, but we can make sure that if a person is in a high-risk group for a disease, they’ll get identified as high risk regardless of what their genetic ancestry is,” Lennon said.
Further Studies, Scoring Implications
With 10 tests in hand, Broad Clinical Labs plans to calculate risk scores for all 25,000 people in the eMERGE network. The researchers also aim to conduct follow-up studies to discover what role polygenic risk scores may play in patients’ overall healthcare.
“Ultimately, the network wants to know what it means for a person to receive information that says they’re at high risk for one of these diseases,” Lennon said.
The researchers’ findings about disease risk are likely also relevant to healthcare systems, which want care teams to make earlier, pre-symptomatic diagnosis to keep patients healthy.
Clinical laboratory leaders may want to follow Broad Clinical Labs’ studies as they perform the 10 genetic tests and capture information about what participants may be willing to do—based on risk scores—to lower their risk for deadly diseases.
