Last month we hosted the webinar “Immune Dysfunction & T-Cell Exhaustion via Single Cell Immune Profiling in ME/CFS & Long COVID,” with Solve Ramsay Research Grant winners Liisa K. Selin, MD, PhD, Anna Gil, PhD (viral immunologists from the Univ. of Massachusetts Chan Medical School), Roshan Kumar, PhD (clinical stage global biotech company HiFiBiO Therapeutics), and the labs’ patient representatives Megan L. Fitzgerald, PhD, and Rivka Solomon, MS. It’s one of our most viewed webinars on YouTube, and it caught the attention of health journalist Cort Johson. Read his coverage of the webinar in Health Rising.
The webinar covered complex scientific information, and our panelists kindly provided a layperson-friendly summary of the material below. It describes the defects these investigators (Selin Lab and HiFiBiO Therapeutics) have found in cells of the immune system from people with ME/CFS and Long COVID. They believe these defects are at the core of ME/CFS and Long COVID.
“First, one of our Patient Representatives, Rivka Solomon, will give a basic description written for the patient community. Then the researchers will give a more advanced summary of their research findings, written for a general audience.
Basic Description for the Patient Community
The findings of researchers Liisa Selin MD PhD, Anna Gil PhD and Roshan Kumar PhD point to something assaulting the immune system of patients with ME/CFS and LC. The assault is ongoing. They don’t yet fully know what that perceptual stimulus is or where it is coming from. Meanwhile, the immune system is working really hard to fight the assault. So hard that the immune system wears itself out and shows markers of exhaustion. (This can be seen in what is called “T cell exhaustion.”) In fact, the immune system becomes so depleted it is no longer able to work properly. And as a result, we feel sick. These collaborating labs are trying to find out what the ongoing assault is, and what it is doing to the immune system. They know the assault changes the immune system, and they can see those changes. In fact, those changes are so clear, they think they could be a biomarker for the disease. Having a biomarker for ME/CFS and Long COVID would validate the disease in the eyes of the medical community and it could be used for diagnosis and to track the progression of the disease. Furthermore, their studies will help identify treatments for our disease.
Researchers’ Summary of Their Research Findings to Date Written for a General Audience
We are a group of qualified and dedicated investigators in viral immunology (Selin/UMass Chan Medical School), molecular biology and immune signatures (Kumar/HiFiBiO) and TcR repertoire analysis (Ghersi/Univ Nebraska). Our complementary expertise makes it likely that we will be successful in our goals:
- Develop a biomarker for infection-associated chronic illness. This is essential to eliminate disbelief by both funding agencies and medical providers
- Identify the mechanism(s) driving immunopathogenesis of infection-associated chronic illness.
Meeting these goals will identify treatment targets and remove the stigma and suffering caused by these diseases. (2021 ME/CFS prevalence estimate in the U.S. alone is ~5M people – more than double AIDS and MS; and there are an estimated 17M or more people in the U.S. with Long COVID).
The perspective of our research on ME/CFS and Long COVID (LC) is that the disease is an aberrant response to an immunological trigger (i.e., infection) that causes a dysregulated immune system. Multiple cellular processes are disrupted, especially immunological and metabolic pathways, but the details of the immunopathology, and why it varies among patients is unknown.
Our results show a partial immunosuppressed state due to overactivation of CD8+ T cells, leading to T cell functional exhaustion. CD8+ T cells are the ‘effector arm’ of the immune system and a critical part of antiviral immune responses, so dysfunctional CD8+ T cells could lead to compromised antiviral immunity and a failure to clear infections. In addition, we found an increase in a unique T cell population that co-express CD4+ and CD8+ markers on their surface. This unusual cell population, although poorly studied, is also increased in several autoimmune diseases and is thought to be prone to autoreactivity because of the potential to recognize a wider set of antigen targets.
Compared to healthy controls, exhausted CD8+ T cells in patients have decreased production of IFNɣ, TNFɑ, and perforin/granzyme, which are all molecules important in controlling any new or persistent infections present such as EBV or CMV. And, we show increased activation markers in patient CD8+ T cells. Taken together, these protein features of patient T cells cluster together and can be easily distinguished from healthy controls using Principal Component Analysis. The patient T cell features are seen in two clusters. Cluster 1 patients have a greater frequency of the unique population of CD4+CD8+ T cells and a lower frequency of CD8+ T cells (majority female) compared to patients in cluster 2 (majority male).
As part of our collaboration, Dr. Roshan Kumar and HiFiBiO Therapeutics have been using single-cell RNA sequencing to measure all of the expressed RNA molecules in individual T cells from patients and healthy controls. This approach allows us to study T cells at a high resolution to better understand how they differ in ME/CFS and LC patients compared to controls. From these data, we see that patients have unique CD8+ T cell subsets compared to controls including unusual populations of exhausted, naïve, and memory “CD4-like” cells. These data are consistent with T cell dysregulation, and they corroborate and expand our T cell functional findings.
Single-cell analysis also allows us to determine the T cell receptor (TcR) sequence of individual T cells. The TcR is the part of a T cell that recognizes its target antigen, and the sequence of a TcR determines what antigens it recognizes. Each person has a particular TcR ‘repertoire’ consisting of billions of T cells with different TcR sequences and antigen specificities. When a T cell recognizes its target antigen it becomes activated and clonally expands, dividing to create many sister T cells with identical TcR sequences and target specificities. By examining the TcR sequences of patients, we can identify groups of T cells that have expanded in response to antigen stimulation. Both the dysfunctional CD4+CD8+ and CD8+ T cell subsets in patients show evidence of clonal expansions to an unknown antigen, which may be a viral or autoantigen. This work is being done in collaboration with Dr. Dario Ghersi at the University of Nebraska at Omaha, who is an expert in TcR repertoire analysis and target antigen prediction. With the combination of single-cell RNA and TcR sequencing data from dysfunctional T cell subsets in patients, we are uniquely positioned to identify the target antigens driving this response which will shed light on underlying disease mechanisms. Altogether, these results suggest that ME/CFS and LC patients have an ongoing, over-activation of CD8+ T cells by some persistent antigen, leading to T cell exhaustion. This is similar to what is observed in a person with chronic viral infections or in tumor environments.
Our studies identify potential biomarkers and mechanisms driving the immunopathogenesis of ME/CFS and LC, which we hope will lead to treatments. Defining the characteristics of the dysfunctional clonally-expanded CD8+ and CD4+CD8+ T cells will be a major advancement in the field and would lead to the identification of specific infectious or auto-antigen triggers that could be the main driver of CD8+ T cell exhaustion and even the immunological basis of ME/CFS and Long COVID.”
Watch the webinar recording here.
View Liisa Selin’s presentation deck here.
View Roshan Kumar’s presentation deck here.
