On March 28, 2024, ImYoo was featured in a ScienceNews article, “How patient-led research could speed up medical innovation.” The biotech startup was showcased for its collaboration with RemissionBiome, a patient-led research project investigating antibiotics as a way to achieve remission for myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). RemissionBiome partnered with ImYoo, which provided their single-cell RNA sequencing (scRNA-seq) discovery platform for an N of 1 study and is now releasing its novel findings.*
*For this N of 1 study, medical and scientific disclaimers are provided at the bottom of this article.
ME/CFS is currently incurable and, by many accounts, “a disease doctors can’t diagnose,” due to its wide-ranging symptoms. In the US, it’s estimated to cost 18 to 24 billion dollars per year in lost productivity and medical costs, and it’s on the rise. For the past year, the National Institutes of Health (NIH) has been designing an ME/CFS research roadmap, which features specialists across eight different medical domains. Doctors, policy makers, and researchers have all been struggling to identify the cause of ME/CFS.
Yet, in this messy disease, ImYoo has spotted a promising signal in one individual. The preliminary results set off a Twitter storm within patient circles, and this model of community-based trials has pharma equally excited.
ImYoo gives patients the tools to painlessly collect their own blood from home. From their patient-centric discovery platform, ImYoo has amassed the largest longitudinal single-cell database from self-collected capillary blood. This fuels their machine learning (ML) models, which enables them to decipher relative changes in gene expression in every immune cell they capture. “It’s like generating a molecular snapshot of your immune system,” says Dr. Tatyana Dobreva, CEO and co-founder of ImYoo. “The more snapshots we capture, the more confident we are in the bigger picture. For this study, we captured 9 snapshots. And from those 9 snapshots, we generated a picture of a dynamic ME/CFS immune system for Tess [Falor], findings that we are eager to share with the community,” she added.
ImYoo x RemissionBiome Collaboration
The RemissionBiome study recruited 50 participants, one of whom is its co-founder, Dr. Tess Falor. A former athlete who had set her sights on becoming an astronaut, Falor developed ME/CFS in 2005 during her time interning at NASA’s Jet Propulsion Labs. She continued with her doctoral degree in Earth and Planetary Sciences, while simultaneously managing her symptoms and immersing herself in the ME/CFS literature. “My husband jokes around that I should have a second PhD in medicine, because of how many research papers I've read,” says Falor.
In 2022, Falor and her co-founder, Tamara Romanuk, began designing and crowdfunding their dual N of 1 study. Falor and Romanuk would take AmoxiClav antibiotics* in the hopes of triggering a “remission event,” what they describe as a sudden elimination of ME/CFS symptoms. In 2007, Falor first experienced one of these events by chance; she called it a “Level 2 remission event.” Falor had taken antibiotics for an unrelated infection and, shortly after, experienced brighter colors and higher energy than she could even recall from her pre-ME/CFS life. “That happened overnight,” Falor recalls. “I went to bed feeling horrible, and when I woke up, I was in that state of remission. It was almost like a switch flipping.”
Falor and Romanuk requested ImYoo’s at-home collection kits to capture molecular snapshots of their immune systems during these remission events. Back in 2007, Falor experienced several of these events at varying durations, from minutes to hours. Flash forward to the RemissionBiome study, and it wasn’t a guarantee that either of them could trigger these events with this intervention. However, with ImYoo’s kits on-hand, they could collect at a moment’s notice.
ImYoo would observe the relative changes in Falor’s and Romanuk’s immune systems, before, during, and after the anticipated remission events. Falor and Romanuk collected their first 3 baseline samples and then commenced their antibiotic intervention. Romanuk did not experience a dramatic remission event. However, Falor did. In fact, she experienced multiple events.
On day 2 of the intervention, Falor experienced a “Level 1 remission event,” characterized by reduced ME/CFS symptoms. She collected a sample for her first event and, on days 5 and 9 of the intervention, she experienced two more remission events and collected samples, respectively. After completing the course of antibiotics, Falor reported the return of milder ME/CFS symptoms compared to her condition before the start of the study. In the approximately two and a half months after stopping the antibiotics, Falor collected 3 more samples at this new baseline.
In total, Falor and Romanuk each captured nine samples. Longitudinal samples, let alone a single ME/CFS sample, are uncommon in the research world. “A lot of people [with ME/CFS] can't leave their house or they're even bed bound,” says Falor. “They can't take part in these research studies where you have to actually travel and go into the clinic,” she adds. To investigate the dramatic shifts in Falor’s symptoms, ImYoo dove deep into the data they generated for her. From these never-before-captured samples, ImYoo conducted its analysis and made a novel finding.
The sample collection schedule from the RemissionBiome N of 1 study. For more details, see the detailed research report.
The Remission Event Results
Supporting existing ME/CFS Research
The results from Falor’s samples, provided in an ImYoo report, coincided with the latest research on ME/CFS and may support some of the existing hypotheses that seek to explain the disease. ImYoo’s analysis flagged CD14 monocytes, also known as classical monocytes, an immune cell type implicated in chronic systemic inflammation. This cell type was also flagged by a Cornell University researcher Dr. Andrew Grimson, whose 2024 study similarly found that this cell type exhibited “the strongest signals of dysregulation” in ME/CFS patients. Together, these findings may provide a specific cell type to strengthen support for the Neuroinflammation Hypothesis of ME/CFS.
On April 11th, Grimson joined the RemissionBiome community for a virtual roundtable discussion. When asked about ImYoo’s findings he commented, “It’s consistent with monocytes being important.”
Grimson was also surprised by how clear ImYoo’s findings were. “There’s really no signal in any other non-monocyte cells?” Grimson asked. “That’s amazing, if that’s true.” To which ImYoo’s CTO, Dr. David Brown responded, “I did the most conservative analysis that we can do… After doing that, there wasn’t anything else that showed up in any of the other cell types.”
ImYoo flags a cell type by the number of gene “hits” it generates in their statistical analysis. The analysis generates a “hit” for every significant shift in a gene’s expression. Gene expression can either go up or down, depending on what functions the cell is executing, and a cell can upregulate or downregulate many genes in parallel. Genes can also interact through these complicated pathways. Despite this complexity, ImYoo’s analysis generated 29 hits, identifying 29 unique genes that changed during Falor’s reported remission event.
“By training machine learning models on our large database of cells, we identify groups of cells that share common features,” explains Brown. “It’s not like we saw genes upregulated everywhere,” he added. “These 29 hits were unique to this cell type. In my opinion, this suggests that there's a specific mechanism at play, rather than broad immune system-wide changes.” It’s possible that, among these 29 hits, lies a novel therapeutic target or biomarker.
Repurposing Existing Drugs and Identifying New Targets
One potential therapeutic target that ImYoo flagged was the gene CCL4. During the remission events, it was downregulated. In accordance with these findings, Grimson’s 2024 paper also correlated ME/CFS symptoms to this gene’s activity. The gene has been studied in animal models, where it was associated with metabolism reprogramming in immune cells. Meanwhile, in human models, Dr. Rob Phair at Stanford University is investigating the Metabolic Trap Hypothesis of ME/CFS. If an antibiotic can target CCL4, then perhaps it can regulate the immune system through these metabolic pathways.
“Your immune system is unique,” says Dobreva. “By measuring it over time, we could one day tailor-make drugs to your biology, or, at the very least, identify or dose existing treatments more appropriately.”
It’s known that antibiotics are a double-edged sword: They can kill bad bacteria, but they can also kill good bacteria. As they fend off infections, these antibiotics can disrupt the immune system. Similar to ImYoo’s observations with the AmoxiClav intervention, various other antibiotics have been shown to slow down monocytes, as well. In healthy individuals, immune disruption is an undesirable effect. But in people with chronic inflammation, it may provide an escape route from vicious feedback loops, like the “metabolic trap.” The outcome of the RemissionBiome study may suggest that immune disruption through antibiotics is a path to controlling hyperactive immune systems.
A box plot showing the reduction in CCL4 gene expression in CD14 monocytes both during and after remission events. For more figures consult the detailed research report.
Through the lens of the microbiome, ImYoo’s findings may connect the dots between ME/CFS and Long COVID, as well. “This is actually really interesting, because it suggests that the microbiome (or microbial metabolites) can impact immune cell activation in this ME/CFS patient,” commented Dr. Lavanya Visvabharathy, a neuroimmunologist at Northwestern University. "This could have implications for Long COVID as well, considering how both conditions occur after viral infections." Long COVID symptoms are often debilitating, persisting in at least 10% of acute COVID infections. The symptoms are similar to that of ME/CFS, with researchers proposing that the two conditions share pathophysiology and even molecular mechanisms.
Steps to treat chronic fatigue through the microbiome are in their promising infancy. In Gulf War Illness (GWI), a common comorbidity with ME/CFS, Dr. Nancy Klimas is investigating fecal transplants as a treatment to repopulate the beneficial bacteria in these patients. It’s also being explored in autoimmune diseases like inflammatory bowel disease (IBD), an indication that ImYoo is currently investigating in its national decentralized studies.
“With our growing database, we hope to connect the dots across autoimmunity,” says Dobreva. “Surely, there are biomarkers that these diseases share. The immune system is the common link, and mapping it out will reframe how we think about disease.”
Next Steps
The results of this RemissionBiome-ImYoo collaboration have seeded hope for a new way of doing research. After completing this N of 1 study, Falor founded RenegadeResearch, a non-profit organization funding community-based studies like this one. They are fundraising to expand this N of 1 study and are also accepting calls for community-based trials in other diseases.
Meanwhile, ImYoo is expanding its platform to research other debilitating diseases with unpredictable, acute events that otherwise wouldn’t be captured in traditional, clinic-based studies. The company has been conducting an internal study in IBD and rheumatoid arthritis (RA) to analyze autoimmune flare-ups from the moment they occur at home. “Like ME/CFS, both IBD and RA flare-ups often prevent patients from getting to the clinic, so we’re excited to see what else we can uncover with timely sampling,” Dobreva shares. As it scales operations, the company is raising its next round of funding.
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The full Remission Biome case study report can be accessed at https://imyoo.health/remissionbiomereport. Data from this study can be downloaded for non-commercial use at https://zenodo.org/records/11100300.
Thank you
Sequencing for this study was generously provided by Complete Genomics. In December 2022, ImYoo was a recipient of their G99 Sponsorship Program. Complete Genomics’ mission is to drive genomics forward with complete sequencing solutions that improve lives. By providing high-quality, cost-effective sequencing, they enable scientists to accelerate genomics research for precision medicine, making it more accessible for physicians and patients.
* Disclaimers
Medical Disclaimer: Both ImYoo and RemissionBiome would like to emphasize that this N of 1 study is not intended to be replicated without proper medical supervision. For that reason, this article does not disclose the details of Falor’s antibiotic regimen. This N of 1 case study is not intended to offer any clinical or scientific advice, nor conclusions, about diseases such as ME/CFS, Long COVID, or any other conditions cited in these writings.
Scientific Disclaimer: ImYoo did not inform the design of this study intervention. Rather, ImYoo’s role was solely to provide observational data and analysis. The observations were made in one individual (i.e. an N of 1 study). Therefore, causality cannot be confirmed from ImYoo’s findings. ImYoo cannot confirm that the observed signals were due to the reported remission event, rather than a typical reaction to antibiotics. To distinguish between disease-specific response and general antibiotic response, ImYoo would suggest an additional study that measures immune response to antibiotic treatment. ImYoo acknowledges that, aside from the RemissionBiome intervention, other factors could have contributed to the results presented in this article. For more resources on how to interpret N of 1 studies, consult this article’s supplementary ImYoo report.
ImYoo’s primary objective of this collaboration was to showcase how at-home sampling can enable patient-led research. From this study, ImYoo demonstrated that longitudinal, molecular data can easily be generated for spontaneous biological events from at-home collections. Consequently, ImYoo generated data to share with their community. As a public benefit corporation, ImYoo’s mission is to engage all stakeholders in the careful process of scientific research and the thrilling prospects of scientific discovery.