title: Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease.
abstract: Lyme disease is a tick-borne illness caused by the bacterium Borrelia burgdorferi, and approximately 10 to 20% of patients report persistent symptoms lasting months to years despite appropriate treatment with antibiotics. To gain insights into the molecular basis of acute Lyme disease and the ensuing development of post-treatment symptoms, we conducted a longitudinal transcriptome study of 29 Lyme disease patients (and 13 matched controls) enrolled at the time of diagnosis and followed for up to 6 months. The differential gene expression signature of Lyme disease following the acute phase of infection persisted for at least 3 weeks and had fewer than 44% differentially expressed genes (DEGs) in common with other infectious or noninfectious syndromes. Early Lyme disease prior to antibiotic therapy was characterized by marked upregulation of Toll-like receptor signaling but lack of activation of the inflammatory T-cell apoptotic and B-cell developmental pathways seen in other acute infectious syndromes. Six months after completion of therapy, Lyme disease patients were found to have 31 to 60% of their pathways in common with three different immune-mediated chronic diseases. No differential gene expression signature was observed between Lyme disease patients with resolved illness to those with persistent symptoms at 6 months post-treatment. The identification of a sustained differential gene expression signature in Lyme disease suggests that a panel of selected human host-based biomarkers may address the need for sensitive clinical diagnostics during the "window period" of infection prior to the appearance of a detectable antibody response and may also inform the development of new therapeutic targets.
  
  
  OBJECTIVE
  Lyme disease is the most common tick-borne infection in the United States, and some patients report lingering symptoms lasting months to years despite antibiotic treatment. To better understand the role of the human host response in acute Lyme disease and the development of post-treatment symptoms, we conducted the first longitudinal gene expression (transcriptome) study of patients enrolled at the time of diagnosis and followed up for up to 6 months after treatment. Importantly, we found that the gene expression signature of early Lyme disease is distinct from that of other acute infectious diseases and persists for at least 3 weeks following infection. This study also uncovered multiple previously undescribed pathways and genes that may be useful in the future as human host biomarkers for diagnosis and that constitute potential targets for the development of new therapies.
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Jerome
authors.initials: J
authors.lastname: Bouquet
authors.affiliation: Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Soloski
authors.affiliation: Department of Biology, San Francisco State University, San Francisco, California, USA.
authors.forename: Andrea
authors.initials: A
authors.lastname: Swei
authors.affiliation: Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Cheadle
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Scot
authors.initials: S
authors.lastname: Federman
authors.affiliation: Qiagen Bioinformatics, Redwood City, California, USA.
authors.forename: Jean-Noel
authors.initials: JN
authors.lastname: Billaud
authors.affiliation: Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
authors.forename: Alison W
authors.initials: AW
authors.lastname: Rebman
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Beniwende
authors.initials: B
authors.lastname: Kabre
authors.affiliation: Qiagen Bioinformatics, Redwood City, California, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Halpert
authors.affiliation: Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
authors.forename: Meher
authors.initials: M
authors.lastname: Boorgula
authors.affiliation: Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA jaucott@jhmi.edu charles.chiu@ucsf.edu.
authors.forename: John N
authors.initials: JN
authors.lastname: Aucott
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA jaucott@jhmi.edu charles.chiu@ucsf.edu.
authors.forename: Charles Y
authors.identifier: http://orcid.org/0000-0003-2915-2094
authors.initials: CY
authors.lastname: Chiu
mesh_terms: D000328:Adult; D000818:Animals; D015415:Biomarkers / Q000097:blood; D025065:Borrelia burgdorferi / Q000502:physiology; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008193:Lyme Disease / Q000175:diagnosis / Q000188:drug therapy / Q000235:genetics* / Q000382:microbiology; D008297:Male; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008875:Middle Aged; D059467:Transcriptome; D014481:United States
chemical_list: D015415:Biomarkers