Persistence and selection of an expanded B-cell clone in the setting of rituximab therapy for Sjögren’s syndrome
© Hershberg et al.; licensee BioMed Central Ltd. 2014
Received: 28 August 2013
Accepted: 13 January 2014
Published: 11 February 2014
Subjects with primary Sjögren’s syndrome (SjS) have an increased risk of developing B-cell lymphoma and may harbor monoclonal B-cell expansions in the peripheral blood. Expanded B-cell clones could be pathogenic, and their persistence could exacerbate disease or predispose toward the development of lymphoma. Therapy with anti-CD20 (rituximab) has the potential to eliminate expanded B-cell clones and thereby potentially ameliorate disease. This study was undertaken to identify and track expanded B-cell clones in the blood of subjects with primary SjS who were treated with rituximab.
To determine whether circulating B-cell clones in subjects with primary SjS emerge or remain after B cell-depleting therapy with rituximab, we studied the antibody heavy-chain repertoire. We performed single-memory B-cell and plasmablast sorting and antibody heavy-chain sequencing in six rituximab-treated SjS subjects over the course of a 1-year follow-up period.
Expanded B-cell clones were identified in four out of the six rituximab-treated SjS subjects, based upon the independent amplification of sequences with identical or highly similar VH, DH, and JH gene segments. We identified one SjS subject with a large expanded B-cell clone that was present prior to therapy and persisted after therapy. Somatic mutations in the clone were numerous but did not increase in frequency over the course of the 1-year follow-up, suggesting that the clone had been present for a long period of time. Intriguingly, a majority of the somatic mutations in the clone were silent, suggesting that the clone was under chronic negative selection.
For some subjects with primary SjS, these data show that (a) expanded B-cell clones are readily identified in the peripheral blood, (b) some clones are not eliminated by rituximab, and (c) persistent clones may be under chronic negative selection or may not be antigen-driven. The analysis of sequence variation among members of an expanded clone may provide a novel means of measuring the chronicity and selection of expanded B-cell populations in humans.
It has been estimated that up to 3 million adults in the US suffer from primary Sjögren’s syndrome (SjS) . Primary SjS is an autoimmune disorder characterized by chronic inflammation of the salivary and lacrimal glands and the presence of antinuclear antibodies, most often of the anti-SSA(Ro) and anti-SSB (La) specificities. Patients are often middle-aged females who present with sicca symptoms, such as dry eyes and dry mouth, fatigue, and joint pain, as well as other extraglandular manifestations, including lung disease and neuropathy. In primary SjS, it is believed that both T cells and B cells contribute to disease pathogenesis. Both cell types infiltrate the salivary and other exocrine glands and show evidence of clonal expansion in the affected tissues as well as the circulation . Notably, there is an increased risk of lymphoma in patients with primary SjS .
Why patients with primary SjS are at increased risk for lymphoma is unclear and has been the subject of several studies (reviewed in ). One theory is that B-cell hyperactivity in primary SjS results in the abnormal activation of autoreactive B-cells and contributes to their clonal expansion . Autoreactive B-cell clones, such as the recently described CD21dim population in SjS, may remain chronically activated instead of anergic in the presence of self-antigens . Autoreactive B-cell clones may also have increased resistance to apoptosis in primary SjS by virtue of elevated levels of the B-cell survival factor, BAFF (B-cell activating factor) . Another theory is that B cells in primary SjS accumulate and persist due to abnormal or inadequate regulation by other cells of the immune system. Borrowing an example from the field of tumor immunology, B cells that are transformed by Epstein-Barr virus are efficiently killed by T cells and natural killer cells . T cells in SjS not only may be derelict in their duties to constrain or kill transformed B cells but may have joined forces with the enemy: SjS T cells are the predominant inflammatory cell population in the exocrine gland lesions, appear to respond to autoantigens on apoptotic cells, secrete pro-inflammatory cytokines, and stimulate B cells (reviewed in ).
Clonal expansions that are evident from abnormalities in the blood may reveal underlying processes that can evolve into a malignant B-cell neoplasia. For example, some patients with monoclonal gammopathy of uncertain significance (MGUS), a condition characterized by the presence of a monoclonal immunoglobulin protein present in the serum, can progress to multiple myeloma . Similarly, a subset of patients with monoclonal B-cell lymphocytosis (MBL), a condition characterized by the presence of a clonal B-cell expansion in the peripheral blood, can progress to chronic lymphocytic leukemia .
We wondered whether a similar spectrum of conditions occurs in primary SjS, with some patients with primary SjS having polyclonal B-cell expansions, others having monoclonal expansions, and still others having transformed monoclonal expansions . Since primary SjS is a systemic autoimmune disease, expanded B-cell clones in the circulation could both be pathogenic (autoreactive) and be linked to an increased risk of lymphoma. However, in primary SjS-associated lymphoma, the B-cell neoplasm is often of the mucosal associated lymphoid tissue (MALT) type . It is not clear whether B-cell populations in the peripheral blood overlap with those in the glands and other tissues, although one intriguing report documents the presence of shared expanded clones in the lymph node tissue and peripheral blood of a patient with SjS who also had marginal zone lymphoma .
The results from several studies suggest that therapy with the B cell-depleting antibody, rituximab (anti-CD20), leads to symptomatic improvement in patients with primary SjS [13–15]. Furthermore, rituximab is known to modulate the antibody repertoire, particularly in antigen-experienced B cells [16, 17]. We therefore reasoned that rituximab therapy might also alter the circulating repertoire of expanded B-cell clones in patients with primary SjS who did not have lymphoma or overt evidence of MGUS or MBL. If CD20 antibody depletion of B cells eliminated expanded B-cell clones and re-set the B-cell repertoire, this approach might favorably modify the disease course in primary SjS by eliminating pathogenic B-cell clones that could be contributing to autoimmunity or predisposing to lymphoma. Conversely, the finding of persistent B-cell clones despite CD20 B-cell depletion therapy with rituximab implies that the restoration of the B-cell repertoire to a pre-disease state is incomplete at best and that the underlying mechanisms responsible for driving the disease process remain unchecked by B-cell depletion. Furthermore, the analysis of diversification by somatic hypermutation of the antibody gene rearrangements within the expanded clone might reveal mechanistic insights into how the clone is being selected (either by self antigen or by negative regulation from the immune system). Therefore, we analyzed the B-cell repertoire of SjS subjects at baseline and after treatment with rituximab by single B-cell sorting and immunoglobulin heavy-chain gene sequencing to identify and molecularly characterize expanded B-cell clones in the blood.
Subjects with primary SjS, as defined by the revised American-European Consensus Group criteria, were enrolled in an open-label Autoimmunity Centers of Excellence-sponsored clinical trial of the B cell-depleting antibody, rituximab (anti-CD20). Clinical features of the study subjects have been described previously . Subjects received two 1-gram doses of rituximab and 100 mg of methylprednisolone on days 0 and 15. For this study, the peripheral blood of six out of the 12 subjects with SjS were studied by flow cytometry, and antibody heavy-chain cloning was performed from single-sorted cells at baseline and at weeks 8, 14, 26, 36, and 52 after the second dose of rituximab . Subjects provided informed consent to participate in this study, which was carried out in accordance with a study protocol that was approved by the institutional review boards of both the Perelman School of Medicine at the University of Pennsylvania and Duke University Medical Center.
Single-cell cloning of immunoglobulin heavy-chain gene rearrangements
Memory and germinal center B-cell subsets (shown in Additional file 1: Figure S1) were recovered from the peripheral blood as described previously [18, 19]. Memory and plasmablast (PB) B-cell subsets were sorted into single wells of 96-well polymerase chain reaction (PCR) plates, and rearranged immunoglobulin heavy-chain (IgH) genes were cloned and sequenced as described previously .
Cloning of the germline VH1-69 immunoglobulin heavy-chain gene rearrangement
Genomic DNA from subject 2 (SjS2) was subjected to PCR amplification with primers that flanked the germline VH1-69 sequence. The primers used were VH1-69 germline forward: 5′-GTG CCC TGA GAG CAT CAC ATA ACA-3′ and VH1-69 germline reverse: 5′-TTC TCC CTC AGG GTT TCT GAC ACT-3′. The cycling conditions were 10 minutes at 94°C, followed by 40 cycles of 94°C for 30 seconds, 58°C for 30 seconds, and 72°C for 30 seconds, followed by 20 minutes at 72°C. Amplicons were TA-cloned (TOPO TA kit; Life Technologies, Grand Island, NY, USA) and sequenced.
Identification of VH, DH, and JH immunoglobulin heavy-chain gene sequences
For each sequenced immunoglobulin gene rearrangement, the most closely matching germline VH, DH, and JH alleles were identified, along with the CDR3 length, functional status (in frame, out of frame, termination codon), and predicted (translated) amino acid sequence by local alignment comparison with the ImMunoGeneTics (IMGT) database . Alignments were verified by using the high-throughput sequencing analysis algorithms from IMGT (V-QUEST version 1.1.2 ), and individual sequences were spot-checked with IgBLAST (National Library of Medicine). To avoid confusing mutations with sequencing imperfections, we considered only positions 10 to 381 of the sequences (by IMGT numbering). The numbers of identifiable IgH variable, diversity and joining (VDJ) rearrangements for each subject at each time point are summarized in Additional file 2: Table S1.
Clonal immunoglobulin gene tree construction
FASTA sequences for all of the clonal variant sequences were analyzed and graphically displayed by using neighbor joining with ClustalX, version 2.1  and by using the default parameters.
Detecting selection from immunoglobulin gene sequence mutation patterns
We used the focused selection test, which is explained in detail in , to detect the forces of selection in the complementarity-determining regions (CDRs) and in the framework regions (FWRs) of the B-cell clones. This test has been shown to be the only one to give reliable and accurate results inferring selection from replacement-to-silent (R/S) ratios  and takes into account micro-sequence specificity [25, 26] and transition bias  in somatic hypermutation. Taking these two factors into account, we calculated for any given set of nucleotides their expected mutability (that is, their relative likelihood to mutate). To estimate the expected level of selection, we count the number of silent mutations in the entire sequence and then use a micro-sequence-based targeting model of somatic mutation as described in  and the actual sequence composition of the mutant’s source germline sequence to estimate the expected number of R mutations [29, 30]. We then used the mutability of the sequence as a background to calculate, under a condition of no selection, the expected rate of R mutations in the area of interest (CDR or FWR) and the S mutations throughout the sequence. In this way, we avoided mixing potentially conflicting forces of selection in FWR and CDR. An overabundance of R mutations was considered an indication of positive selection, and a lack of R mutations was considered an indication of negative selection. When a set of clonally related sequences was analyzed, all unique mutations were grouped together, since mutations that occurred multiple times were probably an indication of common ancestry rather than being mutations that occurred more than once. In this manner, we raised the sensitivity above that obtained by analyzing a single sequence without spuriously counting mutations twice.
We further quantified selection strength by using BASELINe . This algorithm extrapolates the distribution of potential models of selection pressures that could result in the observed patterns of mutation. To accomplish this task, BASELINe considers all mutations from the same condition and considers their origin (clone/sequence/CDR/FWR). In this way, we compared clones with unequal sequence numbers. BASELINe outputs a selection strength (positive or negative) whose certainty is expressed by the width of the distribution curve. All calculations presented here were done with BASELINe’s web version .
We have previously described the results of our open-label pilot trial of rituximab therapy for primary SjS . In this companion study, our goal was to determine whether therapy with rituximab altered or re-set the repertoire in patients with primary SjS, using expanded B-cell clones as a read-out.
B-cell clones are frequent in peripheral blood memory B cells and plasmablasts of rituximab-treated Sjögren’s syndrome subjects
To explore the effects of CD20 B-cell depletion on the B-cell repertoire, antibody heavy-chain gene rearrangements were cloned and sequenced from sorted PBs and memory B cells (see Methods and Additional file 1: Figure S1) of six subjects with SjS before and at various time points after therapy with rituximab. Since B-cell clonal expansions have previously been described in patients with primary SjS [32–34], we reasoned that it would be possible to find and track an expanded B-cell clone in one or more of the subjects over the different study time points.
Here we define clonally related heavy-chain sequences as those that share the same VH (variable), DH (diversity), and JH (joining) gene segments; have the same CDR3 (third complementarity-determining sequence) length; and have highly related CDR3 sequences (identical or differ by only one amino acid or up to three nucleotides). Among the estimated tens of billions of different CDR3 sequences , rearrangements that share the same VH, DH, and JH; have the same CDR3 length; and have highly similar CDR3 sequence overall are very likely to be derived from clonally related B cells. Because the sequences were recovered from single cells, finding the same sequence in two separate cells (which were separately amplified), even if they were obtained at the same time point, was considered to be indicative of clonal expansion.
CDR3 sequence features of expanded B-cell clones
CDR3 (amino acid)
The large clone from SjS2 was identified as an in-frame rearrangement of VH1-69, DH7-27, DH4-23, and JH4-02. Additional file 4: Figure S2 shows the alignment of the most frequently recovered member of the clone with the corresponding germline VH, DH, and JH sequences. We could not account for 10 nucleotides in the CDR3 by their presence in the germline VH, DH, and JH genes. Since these 10 nucleotides were shared in nearly all of the sequences, we inferred that these nucleotides most likely arose by junctional diversification (n- or p-addition) rather than by somatic hypermutation.
Members of the large expanded clone are found in circulating plasmablast and memory B-cell pools
Somatic mutations are frequent in the large expanded clone
To gain further insight into how the expanded clone was selected, we analyzed its pattern of mutation. Although it is possible that some of the intra-clonal variation is due to PCR error, we do not think that PCR error contributes substantially to the sequence diversity of this clone based on the large number of shared mutations between sequences and the ability to independently amplify identical sequences from different B cells.
We also considered the possibility that some of the mutations represented variations in the GL sequence due to the hypothetical presence of an unusual VH1-69 allele in subject SjS2. We therefore cloned the subject’s GL VH1-69 gene by using primers that were present in intronic sequences surrounding the unrearranged VH1-69 gene (see Methods). We obtained only a single VH1-69 sequence out of several independent PCRs (data not shown). Upon alignment (see Methods), the VH sequence matched VH1-69*01 (100% identity, Additional file 4: Figure S2). We therefore conclude that SjS2 is most likely homozygous for the VH1-69*01 allele and that the majority of the sequence differences among different members of the expanded clone are due to somatic hypermutation. Additional file 5: Table S3 summarizes the unique somatic mutations in the members of the expanded clone, relative to the GL sequences for VH1-69*01, JH4-02, and the CDR3 (comprised of DH7-27, DH4-23, and consensus in the areas with presumed n and p nucleotide insertions at the junctions).
Many of the somatic hypermutations in the expanded clone are silent
Observed and expected numbers of unique R and S mutations per time point and overall in the large clone of Sjögren’s syndrome subject 2
CDR R obs
CDR S obs
FWR R obs
FWR S obs
CDR R exp
CDR S exp
FWR R exp
FWR S exp
Clonal expansion is a fundamental property of B cells that participate in an adaptive immune response. In patients with SjS, the identification, characterization, and tracking of expanded B-cell clones over time can provide insights into how clones are selected and whether they are affected by therapy. In this study, we show that expanded B-cell clones are present in the peripheral blood of patients with primary SjS undergoing B-cell depletion therapy with rituximab. There were three main findings: (1) a large expanded clone persisted in the blood of a patient with primary SjS (subject SjS2) despite B-cell depletion with rituximab; this finding indicates that rituximab does not fully re-set the B-cell repertoire in at least some patients with primary SjS; (2) the relative proportion of expanded B-cell clones among sequences recovered from memory and PB cells was highest during the period of maximal B-cell lymphopenia; this finding suggests that the sensitivity for detecting clonal expansions is greatest during periods of iatrogenic or disease-induced lymphopenia; (3) the expanded clones harbored numerous silent mutations; this finding indicates that expanded clones are under negative selection. The frequency and kinds of somatic mutations have potential implications for monitoring the longevity and pathogenic potential of expanded clones in patients with SjS.
Expanded clones are readily detected following rituximab therapy
The presence of expanded B-cell clones and their persistence after rituximab therapy are consistent with the recently reported finding of large persistent B-cell clones in the glands of SjS patients treated with rituximab  and extend the concept of clonal persistence in SjS to the peripheral blood. The expanded B-cell clone in SjS2 persists over the entire 1-year period of the study. It is worth noting that the large clone in SjS2 comprised the highest fraction of the circulating memory B cells during the period of maximal B-cell lymphopenia. This apparent enrichment for the clone during lymphopenia could indicate resistance to rituximab. It is possible that B cells in SjS are intrinsically more resistant to depletion. To this point, autoimmune mice are more resistant to anti-CD20 depletion than wild-type mice , but the exact mechanism is unknown. Memory B cells and PBs (the latter expressing lower levels of CD20 and dominating during the B-cell nadir) may be more resistant to anti-CD20 depletion (reviewed in ). Yet another non-mutually exclusive possibility is that rituximab-resistant B cells reside in protective niches in the secondary lymphoid organs or the exocrine glands and are released with time from these sites during depletion [37, 39]. Another possibility is that the expanded clone undergoes more exuberant homeostatic proliferation during the period of B-cell lymphopenia than polyclonal B cells. The B-lymphopenic state brought about by rituximab therapy is accompanied by increased levels of the B-cell survival factor, BAFF , which, in turn, could relax selection stringency and potentially allow self-reactive or multi-reactive B-cell clones to flourish. In primary SjS, this speculation is particularly apt, as BAFF levels are known to be elevated  and to increase after rituximab therapy in this disease [42, 43], including the current subject cohort and in SjS2 in particular . Furthermore, high BAFF levels appear to correlate with B-cell clonal expansion in the salivary glands and are associated with an increased risk of lymphoproliferative disorders .
Irrespective of the mechanism of clonal resistance, the facile detection of expanded B-cell clones after rituximab therapy points to a possible way to evaluate the risk of lymphoma or the effects of B-cell targeted therapy in patients with primary SjS. It may be easiest to identify expanded clones during the period of B-cell lymphopenia, when there may be a greater opportunity for oligoclonal expansions to be recognized. Selectively surveying the memory B-cell compartment also may have increased the sensitivity of detection of expanded clones, as expanded clones are readily recovered from circulating PBs in vaccinated individuals with intact immune systems .
Molecular features of the expanded clone immunoglobulin heavy-chain rearrangements
The expanded clones recovered from the different subjects with SjS used a variety of VH genes. However, the big clone from SjS2 was interesting because it expressed a VH1-69/JH4 rearrangement with a D-D fusion that could be relevant to the loss of tolerance and disease pathogenesis. The VH1-69 heavy chain includes hydrophobic amino acids in CDR2 that can adopt an unusual conformation and bind a variety of antigens [45, 46]. VH1-69 is frequently used in polyreactive and crossreactive antibody responses to HIV  and in the antibody responses to influenza  and hepatitis C virus (HCV) . Moreover, molecular analysis of antibody gene rearrangements in salivary gland biopsies from patients with SjS reveals increased usage of VH1-69, and even specific H + L chain combinations (VH1-69 + Vκ3-20), that have also been recovered from HCV-associated non-Hodgkin lymphoma cases [49, 50]. IgM+κ+B cells with rheumatoid factor activity are expanded in blood from patients with HCV-associated cryoglobulinemia that express VH1-69/JH4 and Vκ3-20 , suggestive of a common antigenic drive. Vκ3-20 has also been recovered repeatedly in anti-Ro 60 antibodies from separate individual patients with SjS . Of note, SjS2 did have serologic evidence of rheumatoid factor (data not shown) but was HCV-negative and did not have clinical evidence of lymphoma at the time of the rituximab trial.
The D-D fusion found in the SjS2 big clone is fairly uncommon in the normal antibody repertoire, reportedly occurring in approximately 1/800 rearrangements from the blood B cells of healthy individuals ); however, D-D fusions may be more common in autoimmune strains of mice . D-D fusions tend to lengthen the CDR3, although this particular CDR3 sequence is not exceptionally long. The translated CDR3 sequence, which for most members is CARGTGDHTTVVTPFDYW, is highly conserved among the sequence variants of this expanded clone. This sequence, like many other CDR3 sequences, has several hydrophilic residues at the VH end and more hydrophobic residues on the JH end. Whether such a mildly amphipathic sequence with extra length afforded by the second D gene segment can confer greater multireactivity is unclear and may depend critically upon the light chain, which is a major determinant of rheumatoid factor activity [55, 56].
Silent mutations in the expanded clones
The most striking feature is the overall predominance of silent mutations in the heavy-chain sequences among members of the expanded clone, best exemplified in the big clone of subject SjS2. This pattern of mutations is indicative of strong negative selection and may occur because the clone has evolved to the point where it can no longer improve its affinity through mutation; any further replacement mutation thereby might lower the antibody affinity for its antigen. It seems quite clear that whatever characteristic is being ‘protected’ by the negative selection is related to antigen binding given that the negative selection is more pronounced in the CDRs than in the FWRs (Figure 3b, P ≤0.0031). As such, the clone could be highly dependent on a specific antigen. A second possibility is that it is not selection for binding to one antigen but selection for binding to several different antigens that results in a survival advantage. In this scenario, mutations of the CDRs would limit the receptor’s potential interactors, by making it less multireactive. It is intriguing in this respect that some of the commonly encountered autoantigens in systemic autoimmune disease, including the Ro and La antigens that are commonly targeted in SjS, appear to have high degrees of molecular disorder or entropy . Antibody binding to a high-entropy molecule would require a greater activation energy than binding to a lower-entropy molecule and may thereby introduce structural or functional constraints in either the FWR or CDRs. Of course, if the antibody were a rheumatoid factor, it would be able to interact via a wide range of antigens by forming complexes with antibodies bound to other antigens. A third possibility is that the antibody is being selected for some property other than antigen binding, such as the ability to multimerize or self-associate .
In a B-cell that has lost negative regulatory signals from tonic antigen receptor crosslinking, chronic autoantibody crosslinking via persistent self or foreign antigen (model 1), multireactivity (model 2) or antibody self-association (model 3) could promote survival. It is also possible that B cells expressing certain variants of the antibody are kept in check by the immune system. A more detailed analysis of expanded clones and their functional characterization will be needed to distinguish between these intriguing potential modes of negative selection. The existence of negative selection in the CDR serves to remind us that the divisions of CDR and FWR and the impact of mutation are not set in stone. At times, a beneficial mutation may improve antibody affinity by changing an amino acid in the FWR and another mutation may degrade affinity and receptor function by changing an amino acid in the CDR. More generally, high affinity and receptor specificity are not in and of themselves always the goals of somatic selection. As in larger-scale processes of selection that underlie evolution, what determines the function under selection is the specific environment and its constraints.
This study documents the presence of expanded B-cell clones among memory cells and PBs in the circulation of subjects with SjS being treated with rituximab. Expanded clones were readily detected among circulating memory and PB B-cell subsets during periods of B-cell lymphopenia. One SjS subject had an expanded clone that was present prior to and at various times after B-cell depletion therapy. A detailed analysis of the nucleotide sequences of 55 members of this clone revealed a high proportion of silent mutations, suggesting that the clone was under chronic negative selection. Some of the other expanded clones isolated from other rituximab-treated SjS subjects also had frequent silent mutations. The frequency of silent mutations in an expanded clone and its B-cell subset distribution may provide a means of measuring the chronicity and selection of potentially pathogenic B cells in humans.
B-cell activating factor
diversity gene segment
hepatitis C virus
joining gene segment
monoclonal B-cell lymphocytosis
monoclonal gammopathy of uncertain significance
polymerase chain reaction
variable gene segment.
This study was supported by the Autoimmunity Centers of Excellence (U19 AI-056363), a consortium funded by the National Institute of Allergy and Infectious Disease. Additional support was provided by Genentech, Inc., and the Pennsylvania Department of Health. ELP is supported by a grant from the Lupus Research Institute, and WM is the recipient of a postdoctoral fellowship award from the Arthritis Foundation. BZ and UH are supported by a joint Drexel/Hebrew University of Jerusalem, Israel (HUJI) Coulter award. We thank the Autoimmunity Centers of Excellence publications committee for helpful feedback.
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