We analyze and assess BCR repertoires of SLE patients before and after high dose glucocorticoid therapy to address two fundamental questions: (1) After the treatment, how the BCR repertoire of SLE patient change on the clone level? (2) How to screen putative autoantibody clone set from BCR repertoire of SLE patients? The PBMCs of two SLE patients (P1 and P2) at different time points were collected, and DNA of these samples were extracted. of the composition of H-CDR3 showed overall AA compositions of H-CDR3 at three time points in each SLE patients were very similar, and the results of H-CDR3 AA usage that had the same length (14 AA) and the same position were similar. Antinuclear antibody tests of SLE patients showed that level of some antinuclear antibodies reduced after treatment; however, there was no sign that the percentage of autoantibody clones in BCR repertoires would reduce. High dose glucocorticoid treatment in short term will have little impact on composition of BCR repertoire of SLE patient. Treatment can reduce the amount of autoantibody in the protein level, but may not reduce the percentage of autoantibody clones in BCR repertoire in the clonal level. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-1709-4) contains supplementary material, which is available to authorized users. Keywords: SLE, BCR repertoire, H-CDR3, High-throughput sequencing Background Systemic lupus erythematosus (SLE) is an autoimmune disease with unknown etiology and abnormal activation of B cells. Various autoantibodies can be detected in the serum of the SLE patients. Among these autoantibodies, anti-dsDNA, anti-SM and anticardiolipin antibodies have important diagnosis value (Hochberg 1997). It is currently considered that, autoreactive B cell and the autoantibodies LY317615 secreted by plasmocyte are the main factors that directly resulted in pathogen of SLE (Arbuckle et al. 2003). Meanwhile, B cell is also considered as the main target of SLE treatment (Shlomchik et al. 2001; Sanz and Lee LY317615 2010). B cell receptor (BCR), which is on the surface of B cell membrane, LY317615 is an important functional receptor of B cell, involving in immune response of humoral inducing. BCR is a tetrapeptide chain structure with two heavy chains (IGH) and two light chains (IGL). The heavy chain complementary determining region 3 (H-CDR3) is thought to be the key regions of antigen recognition LY317615 and combination (Tonegawa 1983; Chothia et al. 1989; Padlan 1994; Wilson and Stanfield 1994). As for healthy people, peripheral blood often contains about 3??109 BCRs, and the diversity of BCR repertoire or antibody repertoire is produced by multiple mechanism, mainly including rearrangement of various discontinuous V, D and J gene segments (recombination diversity) (Jung et al. 2006), insertion and deletion of nucleotide at VDJ joint (junctional diversity) (Stewart and Schwartz 1994) and somatic hypermutation (SHM) after B cell entering peripheral region (Berek et al. 1991). The past studies have done distinctive analysis on BCR gene composition and rearrangement of SLE and functional study on SLE autoantibody. Kasaian et al. (1994) found that many VH and VL genes taken from anti-DNA IgA autoantibody heavy chain can improve the choice of its SHM. Mockridge et al. (1998) has analyzed on recombination of VH3-34 and VL gene of two SLE patients autoantibody and provided a good basis for studying the length and specificity of CDR3 amino acid (AA). In 1996, Krishnan et al. found that SLE anti-dsDNA autoantibody was closely related to content of arginine of H-CDR3 (Krishnan et al. 1996), and not long after that, found that there was no significant difference in arginine usage of H-CDR3 region in anti-DNA autoantibody between NZBxNZW F1 mice and BALB/c mice in the LY317615 early stage. However, oligoclonal hyperplasia will gradually occur in H-CDR3 of autoantibody rich in arginine in NZBxNZW F1 mice (Krishnan and Marion 1998). Guo et al. who Rabbit Polyclonal to SCAMP1. studied on SLE mouse model found that high affinity antinuclear antibody mainly come from gene recombination, SHM and VH gene replacement of CDR3 region, and that the SHM detection of autoantibody CDR3 region was very important in the study of SLE autoantibody development and B cell differentiation and could provide good monitoring points for SLE (Guo et al. 2010). Although anti-dsDNA and anti-APL are very important in SLE pathology, it is not mean that if there is anti-dsDNA and anti-APL, there will be clinical manifestation. Only there is arginine gathering in IgG CDR3 region, there will be.