Changes in the transcriptome of circulating immune cells of a New Zealand cohort with myalgic encephalomyelitis/chronic fatigue syndrome

Abstract

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a poorly understood disease affecting 0.2%-2% of the global population. To gain insight into the pathophysiology of ME/CFS in New Zealand, we examined the transcriptomes of peripheral blood mononuclear cells by RNA-seq analysis in a small well-characterized patient group (10 patients), with age/gender-matched healthy controls (10 control subjects). Twenty-seven gene transcripts were increased 1.5- to sixfold and six decreased three- to sixfold in the patient group ( P < 0.01). The top enhanced gene transcripts, IL8, NFΚBIA and TNFAIP3, are functionally related to inflammation, and significant changes were validated for IL8 and NFΚBIA by quantitative polymerase chain reaction (qPCR). Functional network analysis of the altered gene transcripts ( P < 0.01) detected interactions between the products related to inflammation, circadian clock function, metabolic dysregulation, cellular stress responses and mitochondrial function. Ingenuity pathway analysis ( P < 0.05) provided further insights into the dysfunctional physiology, highlighting stress and inflammation pathways. This analysis provides novel insights into the molecular changes in ME/CFS and contributes to the understanding of the pathophysiological mechanisms of the disease.

Keywords: chronic fatigue syndrome; circadian rhythm; inflammation; metabolic dysregulation; mitochondrial dysfunction; myalgic encephalomyelitis; oxidative stress; transcriptome.

Figure 1.

(a) Mean fold-change in expression between ME/CFS and controls of IL8, NFKBIA and TNFAIP3 after RT-qPCR assays (±SEM). (b) Scatter plot of normalized triplicate RT-qPCR assay Ct values for each gene in the ME/CFS (n = 10) and control (n = 10) cohorts. The mean Ct value for each gene in the cohorts is also shown (orange line). The Ct value is the PCR amplification cycle at which the gene transcript exceeded the individually calculated baseline threshold level for that gene.

Figure 2.

STRING analysis of significantly altered gene transcripts in the ME/CFS cohort (n = 33, P < 0.01). Protein: protein interaction enrichment network (P = 6.1 × 10⁻⁵) of encoded proteins of differentially expressed gene transcripts in the ME/CFS group compared to controls. Twenty-four functional interactions were identified. Magenta = fusion evidence: genes fused into single open reading frames in other organisms; green = neighbourhood evidence: groups of genes frequently observed in the same chromosomal location; black = co-expression evidence: genes are observed to be correlated in expression across a large number of experiments; light blue = database evidence: known metabolic pathways, protein complexes and so on from curated databases.