Note: Any similarity in this text is due to the maintenance of the original paper’s style. All information credit goes to the authors of the study, as well as supplementary sources.
Xiaotao Shen, Ryan Kellogg, Daniel J. Panyard, Nasim Bararpour, Kevin Erazo Castillo, Brittany Lee-McMullen, Alireza Delfarah, Jessalyn Ubellacker, Sara Ahadi, Yael Rosenberg-Hasson, Ariel Ganz, Kévin Contrepois, Basil Michael, Ian Simms, Chuchu Wang, Daniel Hornburg & Michael P. Snyder
One problem in healthcare today is that treatment is done in response to problems, as opposed to predicting and preventing potential problems. This is especially evident in the way that blood samples are taken. Many limitations, such as infrequent samples due to the cost and discomfort of drawing blood, hinder the ability for early disease detection. As a result, all medical intervention occurs after a disease is diagnosed. But what if these diseases could be detected in advance? This is where a new method called multi-omics microsampling can help provide a more comprehensive look at one’s health. Essentially, this method requires taking small samples of 10 microliters (equivalent to ten-millionths of a liter) frequently. Subsequently, in-depth analysis of the samples is performed by examining thousands of molecules and their environments, or -omes. In this paper, the promise of multi-omics microsampling in detecting responses to diet, as well as creating thorough individual health profiles, is shown.
The instructions for all of the different functions and features of the body are stored in a molecule called DNA, the full set of which is called the genome. When a protein is made, DNA is used to make a transcript of messenger RNA (mRNA), a molecule that is used to make the protein. The collection of all of the mRNA is referred to as the transcriptome. Afterward, the mRNA is translated into a specific protein. Proteins are involved in almost every bodily function. The collection of all of the proteins is referred to as the proteome.
Analyzing these different -omes is important as each collection can reveal different molecules and clues about health. This method of combining different omic groups during analysis is known as multi-omics.
One problem with previous sample methods was that a significant amount of blood (10-50 ml) was required to be drawn with a needle and syringes. To prevent excessive blood loss, these types of samples had to be infrequent, making it difficult to find and analyze rapidly-occurring reactions.
In this research study, however, all samples were drawn using blood pricks of only 10 microliters (equivalent to one-thousandth the amount of blood typically drawn in hospitals). By using a Mitra device, which collects fixed blood samples, the research team could take frequent microsamples. The effectiveness of multi-omics microsampling using this method was shown in two case studies. What should be noted here is that the team used Mass Spectrometry to acquire the molecules in the blood samples. This is because Mass Spectrometry is one of the most sensitive instruments to detect low abundant molecules, and it has been widely used in biomedical studies and clinical applications.
To demonstrate the power of multi-omics microsampling, two case studies were performed exploring two questions.
- How does the body respond in real-time to food?
- How drastically does someone experience molecular changes over a week?
Case study 1: Ensure Shake Response
The responses of different individuals to food are unique and dependent on many factors.
When food is consumed, numerous chemical reactions occur. In the conventional method of sampling, only a few molecules are measured. However, frequent microsampling works well as it can track hundreds of molecules that are found at every moment of the digestive process. This can reveal unprecedented insights into the processes of the digestive system. In this case study, the researchers measured different biological molecules and processes in response to an Ensure shake.
In this study, each “participant collected one microsample (defined as 0 min), consumed the Ensure shake and collected additional blood microsamples at 30, 60, 120 and 240 min after consumption.” Afterward, the biological molecules and -omes were analyzed. A total of 768 compounds were identified for analysis from each individual.
The scientists tracked the effects of Ensure consumption by analyzing the environments of different types of molecules. They found that the response to the Ensure shake was unique to each type of molecule. This is understandable as different molecules are used in diverse ways at distinct times during digestion.
Additionally, statistically significant changes in the levels of numerous molecules occurred after Ensure consumption. For example, it was detected that levels of 115 lipids changed. It was also found that the levels of “99 of the 560 metabolites [examined] significantly shifted following Ensure shake consumption.” This indicates that noticeable differences in molecular responses occurred, and could be detected through multi-omics analysis.
Furthermore, different molecules were grouped into different clusters that corresponded to their concentration pattern (as shown below), as well as their function. In the figures below, it is shown which molecules peaked when and how that corresponds to the biochemical reactions of digestion.
The molecules in cluster 1 included numerous proteins made by the human body. It is clear why the levels of body proteins were so high in a relatively short time. The Ensure shake contained a significant amount of protein. Protein from food is quickly broken down into amino acids, which are protein’s basic building blocks. These are then used to make proteins that the body can use, such as the proteins with peaked levels in cluster 1.
The ability of microsampling to detect molecular activity is evident from the data in cluster 3 (figure g), in which a molecule called acetylcarnitine was shown to decrease. This is because acetylcarnitine is broken down into another molecule called carnitine, which sends fats to the mitochondria, the organelle in the body which extracts energy from food.\
Additionally, a variety of other hormones and molecules were found in the clusters that corresponded to their biochemical function. For example, insulin and gastric inhibitory polypeptide (GIP) were found in cluster 1 with carbohydrates, molecules that are broken into sugars.Insulinis a molecule secreted by the body to manage blood sugar levels, which would otherwise overly increase after carbohydrate intake. GIP is a protein that stimulates insulin. As a result, it is clear why these molecules increased with the levels of carbohydrates, as more insulin is required when there is more sugar in the blood.
Microsampling also revealed many properties of the Ensure shake based on the molecules that appeared in the blood. For example, the Ensure shake was shown to have “anti-inflammatory properties” based on the levels of certain cytokines, immune-related signal proteins involved with inflammation. After consuming the Ensure shake, these cytokine levels declined, showing that this drink can cause a reduction in inflammation. This reveals that certain foods are anti-inflammatory, which can be verified through microsampling.
These findings show the promise of multi-omics microsampling, as more detailed analysis can be done on biological responses and the effects of foods to find more conclusive evidence on beneficial and harmful foods.
Ensure Responses Test
Additionally, the researchers performed a test in which they gave each individual a metabolic score based on their health and molecules present, and found the individuality in the health of each participant. For example, they found that some individuals had connections between the activity of their immune system’s response and signaling molecules related to appetite. Additionally, many individuals showed differences in the activity and levels of certain amino acids and fats, indicating a large amount of variability in the processes that make these molecules among individuals. These findings are important as an understanding of individual health responses can help us better treat and prevent diseases.
Case study 2: 24/7 Individual Profiling
Many studies have taken high-volume blood samples to build health profiles for individuals. However, due to infrequent samples, these samples cannot follow patterns that affect the levels of certain body molecules. Patterns such as circadian rhythm (the body’s clock mechanism) and other complex patterns can only be observed through frequent samples.
In this case study, one participant was subject to numerous microsamples every day for a total of 98 microsamples over 7 days.
This multi-omics microsampling technique was effective and in-depth, as it detected 2,213 molecules and took 214,661 measurements (numerous measurements for each type of molecule and process), in addition to data from wearable devices.
Additionally, the researchers found that the content of sugars in microsamples was the same as in the food consumed, showing the precision in this type of analysis.
Wearable and Multi-Omics Data Reveal New Findings
The researchers first aimed to test whether the data from the wearable devices and multi-omics microsamples reflect the health patterns of an individual. The 2,213 molecules were grouped based on events they were involved in, such as circadian rhythms (biological clock), or other time-related patterns. It was found that specific lipids and metabolites were related to the biological clock patterns, demonstrating that different molecules operate on different time patterns and rhythms that are unique.
Additionally, cortisol, a hormone associated with stress, was analyzed, and its levels varied and didn’t exhibit any pattern. This went against the common belief that cortisol levels fluctuate based only on the time. This finding is significant as it shows how multi-omics microsampling can reveal more about an individual’s stress profile. Furthermore, findings like this can have major clinical implications, given the relationship between cortisol, stress, and death.
The levels of many other molecules at a certain time matched the scientific explanation for their appearance, showing the accuracy of the microsampling method.
The Detail of Wearable and Multi-Omics Data
Combining wearable data and multi-omics microsampling can allow us to analyze minute changes in the body, which was not previously possible with infrequent sampling methods. In this study, researchers matched the data from the wearable devices to the microsampling data points. They found that sugar levels and immune responses were correlated. However, they found some immune-related proteins that were exceptions. They also observed certain molecules which allowed them to develop a more detailed understanding of how energy is broken down in an individual. For example, changes in levels of glucagon (stored version of glucose) accurately reflected how it was being broken down to be used for energy. These findings show that frequent microsampling is essential as it allows us to detect many individual details and differences that would not be otherwise possible through conventional sampling.
Wearables provide continuous health monitoring through surface-level tests such as heart rate, whereas microsamples provide more information on the microscale through dynamic internal information on specific molecules. This fascinating combination of the macroscopic and microscopic view of the body can help paint the full picture of a human’s health profile, allowing better disease prediction and assessment.
As the two case studies demonstrate, multi-omics microsampling is a revolutionary new procedure that will allow individuals to receive more personalized care. This is extremely important as each individual’s experiences and environments are different. Environmental variation can affect what proteins are made by the body, and how the body functions as a result. Additionally, frequent sampling with comprehensive multi-omics analysis allows for many diseases to be detected in advance, which can reduce the number of patients in hospitals. This connects to the objective of multi-omics, which is to deliver predictive measures that can prevent diseases. As the depth of analysis continues to increase, it is clear that the future of healthcare and the ability to predict and treat diseases in advance lies in multi-omics microsampling.
Shen, X., Kellogg, R., Panyard, D.J., Bararpour, N. et al. Multi-omics microsampling for the profiling of lifestyle-associated changes in health. Nat. Biomed. Eng (2023). https://doi.org/10.1038/s41551-022-00999-8
Che, Fa-Yun, et al. “Mass Spectrometry Applications in Biomedical Research – PMC.” NCBI, 5 April 2015, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4454730/ . Accessed 8 June 2023.
“Cytokines and Their Side Effects.” American Cancer Society, 27 December 2019, https://www.cancer.org/treatment/treatments-and-side-effects/treatment-types/immunotherapy/cytokines.html . Accessed 8 June 2023.
“Definition of Metabolite – NCI Dictionary of Cancer Terms – NCI.” National Cancer Institute, https://www.cancer.gov/publications/dictionaries/cancer-terms/def/metabolite . Accessed 8 June 2023.
Neoteryx. “DBS and the Hematocrit Bias: A Brief Introduction.” Neoteryx, 22 March 2018, https://www.neoteryx.com/microsampling-blog/the-hematocrit-bias-a-very-brief-introduction . Accessed 8 June 2023.
Neoteryx. “How to Use The Mitra Cartridge | Remote Microsampling Device.” YouTube, 22 April 2019, https://www.youtube.com/watch?v=klXPo0g-2o4 . Accessed 8 June 2023.
Sarmento, Maria J., et al. “Comparison of Single Phase and Biphasic Extraction Protocols for Lipidomic Studies Using Human Plasma.” Frontiers, 29 July 2019, https://www.frontiersin.org/articles/10.3389/fneur.2019.00879/full . Accessed 8 June 2023.
Badri Viswanathan is a junior at Hillsdale High School. He is extremely interested in the promise of genomics and other scientific breakthroughs, especially as pertaining to cardiology. He is the founder and president of a club at his school called Medicine for Us!, in which scientific literature is condensed and analyzed. This research is then shared to the community through monthly presentations.
In collaboration with the Stanford Healthcare Innovation Lab, he furthers his mission by analyzing promising new findings, such as multi-omics research. Badri hopes to be a cardiologist and conduct research one day.