Thesis Molecular Epidemiologic Studies of Myalgic Encephalomyelitis (ME) / Chronic Fatigue Syndrome (CFS), 2025, Kumar

[ Embargoed PhD thesis; abstract only. ]

Abstract
Background: Myalgic encephalomyelitis (ME)/chronic fatigue syndrome (CFS) is a disabling multisystem complex disorder with no known etiology or approved treatment. Our studies aimed to assess the link between ME/CFS and autoimmune disease (AID) and cancer, and to identify potential biomarkers and biological mechanisms to further explore pathophysiology of this diseases.

Methods: All analyses were done using data from a case-control study of ME/CFS conducted by Dr. Roxana Moslehi and her collaborators. In our first study we estimated the cumulative incidences of AID and cancer among first degree relatives of 60 cases and 61 controls and compared cumulative incidences using Fine‐Gray sub distribution hazard model.

In our second study we compared the levels of 48 serum cytokines between cases and controls using logistic regression and 4 different machine learning classifier algorithms to identify cytokines discriminating cases from controls.

In our third study we quantified gene expression from the raw RNA-Seq reads from Illumina sequencing of 60 ME/CFS cases and 60 matched controls using the protocol developed by Dr. Moslehi and one of her collaborators on this project. The gene expression profiles were compared using a generalized linear model fit with t-test to identify differentially expressed genes (DEG). Gene Set Enrichment Analysis (GSEA) was performed on DEG to explore pathways involved.

Results: The risk of any AID diagnosis among first degree relatives of cases was 3.52 time higher than the first-degree relatives of controls (p-value = 0.001) and it was 2.68 time higher after excluding ME/CFS from the definition of AIDs (p-value = 0.023). The cumulative incidence of any cancer among first degree relatives of cases and controls was not statistically different (p-value = 0.28). After limiting the age of follow up at 60 years, the risk of any cancer diagnosis among first degree relatives of cases was 2.24 time higher than the first-degree relatives of controls (p-value = 0.03). The cumulative incidence of blood cancer among first degree relatives of cases was 3% at the follow up to 60 years and it was statistically different (p-value=0.04).

For our study on comparison of cytokine expressions, in bivariate comparison, ME/CFS cases had significantly lower plasma levels of Fractalkine (p=0.04), IL-6 (p=0.05), MIP-1α (p=0.05) and the levels of IP-10, IL-12p40, and TNFα, were lower in cases but with borderline significance. In contrast, RANTES (CCL5), was increased in the ME/CFS case group as compared to controls (OR=1.76, p-value=0.08). The sum of the scaled variable importance scores (VIP) from 3 models found 5 cytokines IL-27 (VIP =7.07), IP-10 (VIP=6.97), IL-8 (3.87), IL-12p70 (VIP=1.48), and IL-6 (VIP=0.85) with high importance in all 3 models and RANTES (VIP=4.29), IL-12p40 (VIP=3.11), Fractalkine (VIP=2.85), MIP-1β (VIP=1.94), IL-1β (VIP=1.41), IFN-α2 (VIP=1.18), GROα (VIP=1.07), M-CSF (VIP=0.96), MIG/CXCL9 (VIP=0.90), and PDGF-AB/BB (VIP=0.85) in 2 of the models with a higher importance.

In comparing RNA-sequencing data initial analysis revealed very low number of differentially expressed genes (DEG), but after batch correction for gender and samples with higher per sequence GC content, we found 93 differentially expressed genes below the FDR of 0.2. 51 genes were upregulated and 42 were downregulated in ME/CFS cases compared to controls. The DEGs were involved in immune dysregulation, neuroinflammation and neurological dysfunction, and metabolic dysregulation. GSEA analysis revealed 23 canonical pathways with FDR below 0.10.

Conclusion: Our findings revealed higher cumulative incidence of AIDs among first degree relatives of cases and increased risk of AIDs among first degree relatives of ME/CFS cases suggesting a link between ME/CFS and AID. The cumulative incidence of early onset cancers including blood cancers were also higher among first degree relatives of cases and risk of early onset cancers were higher in first degree relatives of ME/CFS cases. Our second study revealed a set of potential biomarkers reflecting the complex interplay between immune dysregulation, chronic inflammation, and tissue remodeling that underlies many of the debilitating symptoms of ME/CFS. However, further validation from proteomics and high throughput RNA-sequencing studies is required to clarify their precise roles and how they might be targeted therapeutically in ME/CFS. Our RNA sequencing analysis provides clues into the DEGs, and biologic pathways involved in ME/CFS.

Finding potential biomarkers for ME/CFS has significant public health relevance as it can lead to early detection, in personalizing treatment approaches, better understanding of comorbidities, and thus dramatically reducing healthcare burden.

___
Kumar, Anil, "Molecular Epidemiologic Studies of Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS)" (2025). Electronic Theses & Dissertations (2024 - present). 173.
https://scholarsarchive.library.albany.edu/etd/173
Available for download on Friday, May 01, 2026