A SWATH-MS analysis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome peripheral blood mononuclear cell proteomes reveals mitochondrial dysfunction

Abstract

Background Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a serious and complex physical illness that affects all body systems with a multiplicity of symptoms, but key hallmarks of the disease are pervasive fatigue and ‘post-exertional malaise’, exacerbation after physical and/or mental activity of the intrinsic fatigue and other symptoms that can be highly debilitating and last from days to months. Although the disease can vary widely between individuals, common symptoms also include pain, cognitive deficits, sleep dysfunction, as well as immune, neurological and autonomic symptoms. Typically, it is a very isolating illness socially, carrying a stigma because of the lack of understanding of the cause and pathophysiology. Methods To gain insight into the pathophysiology of ME/CFS, we examined the proteomes of peripheral blood mononuclear cells (PBMCs) by SWATH-MS analysis in a small well-characterised group of patients and matched controls. A principal component analysis (PCA) was used to stratify groups based on protein abundance patterns, which clearly segregated the majority of the ME/CFS patients (9/11) from the controls. This majority subgroup of ME/CFS patients was then further compared to the control group. Results A total of 60 proteins in the ME/CFS patients were differentially expressed (P < 0.01, Log10 (Fold Change) > 0.2 and < −0.2). Comparison of the PCA selected subgroup of ME/CFS patients (9/11) with controls increased the number of proteins differentially expressed to 99. Of particular relevance to the core symptoms of fatigue and post-exertional malaise experienced in ME/CFS, a proportion of the identified proteins in the ME/CFS groups were involved in mitochondrial function, oxidative phosphorylation, electron transport chain complexes, and redox regulation. A significant number were also involved in previously implicated disturbances in ME/CFS, such as the immune inflammatory response, DNA methylation, apoptosis and proteasome activation. Conclusions The results from this study support a model of deficient ATP production in ME/CFS, compensated for by upregulation of immediate pathways upstream of Complex V that would suggest an elevation of oxidative stress. This study and others have found evidence of a distinct pathology in ME/CFS that holds promise for developing diagnostic biomarkers.

Dysregulated Provision of Oxidisable Substrates to the Mitochondria in ME/CFS Lymphoblasts

“…Within the regulatory regions of protein-coding genes investigated in the Helliwell study, it is worthwhile noting that the gene encoding the Complex 1 subunit NDUFA11 was hypomethylated [ 84 ]. This is consistent with the elevated Complex 1 expression evident in this and our previous study of lymphoblasts [ 2 ], as well as the same authors’ study of PBMCs [ 66 ]. Continued epigenetic studies utilising different cell types would be valuable, since it may be possible that in proliferative cell types such as lymphoblasts, factors such as altered gene expression programmes or glutamine depletion are accentuated and thus may impact DNA methylation status to a greater degree than in PBMCs.…”

“…Similarly, elevated fatty acid β-oxidation suggested by Germain et al is also consistent with our observations here, if the rates of fatty acid β-oxidation are indeed upregulated in accordance with expression of the enzymes involved [10]. Sweetman et al observed elevated levels of enzymes involved in ketone body metabolism in the proteomes of ME/CFS PBMCs, which could indicate increased oxidation of fatty acids and their derivatives through the TCA cycle [66]. More strikingly within this same study, acyl-CoA dehydrogenases and the beta subunit of mitochondrial trifunctional enzyme (HADHB), specifically, were elevated in their expression in PBMCs [66]-an observation shared in our own work here with lymphoblasts.…”

“…Sweetman et al observed elevated levels of enzymes involved in ketone body metabolism in the proteomes of ME/CFS PBMCs, which could indicate increased oxidation of fatty acids and their derivatives through the TCA cycle [66]. More strikingly within this same study, acyl-CoA dehydrogenases and the beta subunit of mitochondrial trifunctional enzyme (HADHB), specifically, were elevated in their expression in PBMCs [66]-an observation shared in our own work here with lymphoblasts. This is in addition to shared observations of elevated expression of OXPHOS complex subunits-prominently Complexes I and V-and proteins in substrate-providing pathways such as the TCA cycle [66].…”

“…The elevated expression of proteasome subunits and assembly factors in ME/CFS lymphoblasts suggests that targeted protein degradation is upregulated. The recent proteomic study by Sweetman et al [ 66 ] also reported elevated expression of proteasome subunits and assembly factors in ME/CFS PBMCs. Together with our results, this provides compelling evidence that the ubiquitin-proteasome system is upregulated in lymphoid cells from ME/CFS patients.…”

“…While no members of the prolyl hydroxylase family were detected in the whole-cell proteomics experiments, SLC25A11 was well detected and significantly elevated in its expression ( Figure S3 ). SLC25A11 is one of the mitochondrial transport proteins we previously reported to be upregulated in ME/CFS lymphoblasts [ 2 ] and it was also found to be upregulated in PBMCs by Sweetman et al [ 66 ].…”