title: Longitudinal analysis of peripheral blood T cell receptor diversity in patients with systemic lupus erythematosus by next-generation sequencing.
abstract: BACKGROUND
  T cells play an important role in the pathogenesis of systemic lupus erythematosus (SLE). Clonal expansion of T cells correlating with disease activity has been observed in peripheral blood (PB) of SLE subjects. Recently, next-generation sequencing (NGS) of the T cell receptor (TCR) β loci has emerged as a sensitive way to measure the T cell repertoire. In this study, we utilized NGS to assess whether changes in T cell repertoire diversity in PB of SLE patients correlate with or predict changes in disease activity.
  
  
  METHODS
  Total RNA was isolated from the PB of 11 SLE patients. Each subject had three samples, collected at periods of clinical quiescence and at a flare. Twelve age-matched healthy controls (HC) were used for reference. NGS was used to profile the complementarity-determining region 3 (CDR3) of the rearranged TCR β loci.
  
  
  RESULTS
  Relative to the HC, SLE patients (at quiescence) demonstrated a 2.2-fold reduction in repertoire diversity in a given PB volume (P <0.0002), a more uneven distribution of the repertoire (Gini coefficient, HC vs SLE, P = 0.015), and a trend toward increased percentage of expanded clones in the repertoire (clone size >1.0%, HC vs SLE, P = 0.078). No significant correlation between the overall repertoire diversity and clinical disease activity was observed for most SLE patients with only two of eleven SLE patients showing a decreasing trend in repertoire diversity approaching the flare time point. We did not observe any overlap of CDR3 amino acid sequences or a preferential Vβ or Jβ gene usage among the top 100 expanded clones from all SLE patients. In both HC and SLE, the majority of the expanded clones were remarkably stable over time (HC = 5.5 ±0.5 months, SLE = 7.2 ±2.4 months).
  
  
  CONCLUSIONS
  A significant decrease in T cell repertoire diversity was observed in PB of SLE patients compared to HC. However, in most SLE patients, repertoire diversity did not change significantly with increases in disease activity to a flare. Thus, without a priori knowledge of disease-specific clones, monitoring TCR repertoire in PB from SLE patients is not likely to be useful to predict changes in disease activity.
authors.affiliation: Biogen, 250 Binney Street, Cambridge, MA, 02142, USA. Dharma.Thapa@biogenidec.com.
authors.forename: Dharma R
authors.initials: DR
authors.lastname: Thapa
authors.affiliation: Biogen, 250 Binney Street, Cambridge, MA, 02142, USA. Raffi.Tonikian@gmail.com.|Novartis Pharmaceuticals Canada Inc, 385 Bouchard Boulevard, Dorval, QC, H9S 1A9, Canada. Raffi.Tonikian@gmail.com.
authors.forename: Raffi
authors.initials: R
authors.lastname: Tonikian
authors.affiliation: Biogen, 250 Binney Street, Cambridge, MA, 02142, USA. Chao.Sun@biogenidec.com.
authors.forename: Chao
authors.initials: C
authors.lastname: Sun
authors.affiliation: Biogen, 250 Binney Street, Cambridge, MA, 02142, USA. Mei.Liu@biogenidec.com.
authors.forename: Mei
authors.initials: M
authors.lastname: Liu
authors.affiliation: Biogen, 250 Binney Street, Cambridge, MA, 02142, USA. Andrea.Dearth@biogenidec.com.
authors.forename: Andrea
authors.initials: A
authors.lastname: Dearth
authors.affiliation: Johns Hopkins University School of Medicine, 1830 East Monument Street, Baltimore, MD, 21205, USA. MPetri@jhmi.edu.
authors.forename: Michelle
authors.initials: M
authors.lastname: Petri
authors.affiliation: Adaptive Biotechnologies, 1551 Eastlake Avenue East, Seattle, WA, 98102, USA. FPepin@adaptivebiotech.com.
authors.forename: Francois
authors.initials: F
authors.lastname: Pepin
authors.affiliation: Adaptive Biotechnologies, 1551 Eastlake Avenue East, Seattle, WA, 98102, USA. REmerson@adaptivebiotech.com.
authors.forename: Ryan O
authors.initials: RO
authors.lastname: Emerson
authors.affiliation: Biogen, 250 Binney Street, Cambridge, MA, 02142, USA. Ann.Ranger@biogenidec.com.
authors.forename: Ann
authors.initials: A
authors.lastname: Ranger
mesh_terms: D000328:Adult; D022801:Complementarity Determining Regions / Q000235:genetics / Q000276:immunology; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008137:Longitudinal Studies; D008180:Lupus Erythematosus, Systemic / Q000235:genetics* / Q000276:immunology*; D008297:Male; D008875:Middle Aged; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics* / Q000276:immunology*
chemical_list: D022801:Complementarity Determining Regions; D016693:Receptors, Antigen, T-Cell, alpha-beta