RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease Authors: Jerome Bouquet, Jennifer L. Gardy, Scott Brown, Jacob Pfeil, Ruth R. Miller, Muhammad Morshed, Antonio Avina-Zubieta, Kam Shojania, Mark McCabe, Shoshana Parker, Miguel Uyaguari, Scot Federman, Patrick Tang, Ted Steiner, Michael Otterstater, Rob Holt, Richard Moore, Charles Y. Chiu, David M. Patrick for the Complex Chronic Disease Study Group (Vancouver, BC, Canada) Clin Infect Dis (2017) ciw767. DOI:https://doi.org/10.1093/cid/ciw767 Published: 18 January 2017 Article history: Received: 25 August 2016 Accepted: 27 December 2016 Abstract Background. Chronic fatigue syndrome (CFS) remains poorly understood. Although infections are speculated to trigger the syndrome, a specific infectious agent and underlying pathophysiological mechanism remain elusive. In a previous study, we described similar clinical phenotypes in CFS patients and alternatively diagnosed chronic Lyme syndrome (ADCLS) patients—individuals diagnosed with Lyme disease by testing from private Lyme specialty laboratories but who test negative by reference 2-tiered serologic analysis. Methods. Here, we performed blinded RNA-seq analysis of whole blood collected from 25 adults diagnosed with CFS and 13 ADCLS patients, comparing these cases to 25 matched controls and 11 patients with well-controlled systemic lupus erythematosus (SLE). Samples were collected at patient enrollment and not during acute symptom flares. RNA-seq data were used to study host gene expression, B-cell/T-cell receptor profiles (BCR/TCR), and potential viral infections. Results. No differentially expressed genes (DEGs) were found to be significant when CFS or ADCLS cases were compared to controls. Forty-two DEGs were found when SLE cases were compared to controls, consistent with activation of interferon signaling pathways associated with SLE disease. BCR/TCR repertoire analysis did not show significant differences between CFS and controls or ADCLS and controls. Finally, viral sequences corresponding to anelloviruses, human pegivirus 1, herpesviruses, and papillomaviruses were detected in RNA-seq data, but proportions were similar (P = .73) across all genus-level taxonomic categories. Conclusions. Our observations do not support a theory of transcriptionally mediated immune cell dysregulation in CFS and ADCLS, at least outside of periods of acute symptom flares.