SUMMARY The symptoms of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) typically wax and wane. Our objective in this project is to identify biomarkers that correlate with fluctuations in clinical status and have the potential to yield insights into pathogenesis that enable interventions. Sixty people with ME/CFS followed in a large New York City practice and 60 healthy controls matched +/- 5 years for age, sex, and socioeconomic status, will use a smartphone application to regularly report the severity of their symptoms, and whether they are having a particularly good or bad day. Immediately after a person enters data, the information will be sent to the study server and (on good and bad days) to a study coordinator/phlebotomist who will contact the individual to visit the subject’s location to obtain blood, saliva, and feces within 24 hours. We will pursue biomarker discovery on good and bad days. We will profile multiple cytokines previously found to be abnormal in ME/CFS; quantitate the prevalence and abundance of microbial sequences in plasma, saliva, and feces using capture sequencing; assay levels of antibodies to specific target epitopes using a state-of-the-art phage display system; and perform single cell RNASeq analyses of B cells, T cells, dendritic cells, NK cells and the recently discovered Kir+CD8+ regulatory T cells. Metabolomic and lipidomic studies will be conducted in plasma, saliva, and feces to determine if abnormalities, that we and others have previously identified, improve on good days and worsen on bad days. These include evidence of peroxisomal dysfunction (decreased levels of plasmalogens, unsaturated phospholipid ethers and carnitines and increased levels of polyunsaturated long-chain triacylglycerides); consistently reduced plasma levels of prostaglandin F2 alpha, the oxylipin resolvin D1 and phosphatidylcholines (PCs); significant elevations in α-ketoglutarate (α-KG) and succinate (TCA cycle intermediates). Collectively, these changes may contribute to mitochondrial dysfunction/impaired ATP generation and the pro-inflammatory state that have been found in ME/CFS. Fecal metabolomics allow measurement of very short chain fatty acids, a clear indicator of differences in fermentative energy metabolism, and measurement of physiologically relevant microbial products that impact carbohydrate metabolism and immune function. In collaboration with Alain Moreau at ICanCME in Montreal, we will assess microRNA expression to determine whether previously identified abnormalities improve on good days and worsen on bad days.

PROJECT NARRATIVE People with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) have “good days” and “bad days”. In this project people, with ME/CFS will report good and bad days using a smartphone application that will prompt a coordinator to make a site visit convenient for the patient and collect clinical information as well as biological samples for comprehensive analyses. Results will be used to identify factors associated with improvement or deterioration of health status that are anticipated to lead to new insights in strategies for intervention in ME/CFS.