Longitudinal analysis of peripheral blood T cell receptor diversity in patients with systemic lupus erythematosus by next-generation sequencing

Dharma R Thapa, Raffi Tonikian, Chao Sun, Mei Liu, Andrea Dearth, Michelle Petri, Francois Pepin, Ryan O Emerson, Ann Ranger

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. 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. 12 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. 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 towards 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 2 of 11 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 amongst 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). 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.