Transcriptional reprogramming primes CD8+ T cells towards exhaustion in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome [ATAC-seq]

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME) is a severe, debilitating disease, with mounting evidence pointing to immune dysregulation as a key contributor to pathophysiology. To characterize the gene regulatory state underlying dysregulation of T cells in ME, we performed multiomic analysis of distinct subsets by integrating single-cell RNA-seq, RNA-seq and ATAC-seq, and further analyzed CD8+ T cell subpopulations following symptom provocation. Certain subsets of CD8+ T cells, as well as certain innate lineages of T cells, displayed the most pronounced dysregulation in ME. We observed upregulation of key transcription factors associated with T cell exhaustion in CD8+ T cell effector memory subsets, as well as an altered chromatin landscape and metabolic reprogramming consistent with an exhausted immune cell state. To validate these observations, we analyzed expression of exhaustion markers using flow cytometry, detecting a higher frequency of exhaustion-associated transcription factors, and supporting a novel state of immune dysregulation in ME, which may ultimately provide a basis for future therapies. Overall design: RNA-seq and ATAC-seq were performed on FACS purified naive (CD45RA+CCR7+) and antigen-experienced (CD45RA-CCR7+/-) CD8+ T cells from 7 ME patients and 7 healthy sedentary controls.