RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.
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.



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.



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.



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.
Department of Laboratory Medicine, University of California, San Francisco, USA.
Jerome
J
Bouquet
Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada.|School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.
Jennifer L
JL
Gardy
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada.|Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada.
Scott
S
Brown
Department of Laboratory Medicine, University of California, San Francisco, USA.
Jacob
J
Pfeil
School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.
Ruth R
RR
Miller
British Columbia Centre for Disease Control Public Health Laboratory, 655 W 12th Ave., Vancouver, British Columbia, Canada.|Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, Vancouver, British Columbia, Canada.
Muhammad
M
Morshed
Department of Medicine, Division of Rheumatology, University of British Columbia, Vancouver, BC, Canada.
Antonio
A
Avina-Zubieta
Department of Medicine, Division of Rheumatology, University of British Columbia, Vancouver, BC, Canada.
Kam
K
Shojania
Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada.
Mark
M
McCabe
Centre for Health Evaluation Outcome Sciences, Vancouver, Canada.
Shoshana
S
Parker
Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada.
Miguel
M
Uyaguari
Department of Laboratory Medicine, University of California, San Francisco, USA.
Scot
S
Federman
Department of Pathology, Sidra Medical and Research Centre, Doha, Qatar.
Patrick
P
Tang
Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, Canada.
Ted
T
Steiner
Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada.|School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.
Michael
M
Otterstater
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada.
Rob
R
Holt
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada.
Richard
R
Moore
Department of Laboratory Medicine, University of California, San Francisco, USA.|Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, USA.
Charles Y
CY
Chiu
Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada.|School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.
David M
DM
Patrick
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001402:B-Lymphocytes / Q000276:immunology / Q000378:metabolism; D016022:Case-Control Studies; D002908:Chronic Disease; D004198:Disease Susceptibility; D015673:Fatigue Syndrome, Chronic / Q000209:etiology*; D005260:Female; D015870:Gene Expression; D020869:Gene Expression Profiling; D020022:Genetic Predisposition to Disease; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions / Q000235:genetics* / Q000276:immunology; D006801:Humans; D008193:Lyme Disease / Q000209:etiology*; D008297:Male; D054892:Metagenome; D056186:Metagenomics / Q000379:methods; D010641:Phenotype; D011947:Receptors, Antigen, B-Cell / Q000737:chemistry / Q000235:genetics*; D011948:Receptors, Antigen, T-Cell / Q000737:chemistry / Q000235:genetics*; D013601:T-Lymphocytes / Q000276:immunology / Q000378:metabolism; D014777:Virus Diseases / Q000150:complications* / Q000821:virology
D011947:Receptors, Antigen, B-Cell; D011948:Receptors, Antigen, T-Cell
chronic fatigue syndrome; RNA-seq; transcriptome; viral infection; B-cell/T-cell receptors