Immunoglobulin variable-region gene mutational lineage tree analysis: application to autoimmune diseases

Lineage trees have frequently been drawn to illustrate diversification, via somatic hypermutation (SHM), of immunoglobulin variable-region (IGV) genes. In order to extract more information from IGV sequences, we developed a novel mathematical method for analyzing the graphical properties of IgV gene lineage trees, allowing quantification of the differences between the dynamics of SHM and antigen-driven selection in different lymphoid tissues, species, and disease situations. Here, we investigated trees generated from published IGV sequence data from B cell clones participating in autoimmune responses in patients with Myasthenia Gravis (MG), Rheumatoid Arthritis (RA), and Sjögren's Syndrome (SS). At present, as no standards exist for cell sampling and sequence extraction methods, data obtained by different research groups from two studies of the same disease often vary considerably. Nevertheless, based on comparisons of data groups within individual studies, we show here that lineage trees from different individual patients are often similar and can be grouped together, as can trees from two different tissues in the same patient, and even from IgG- and IgA-expressing B cell clones. Additionally, lineage trees from most studies reflect the chronic character of autoimmune diseases

Multimodal interventions to enhance adherence to secondary preventive medication after stroke: a systematic review and meta-analyses

Summary: Introduction: Nonadherence to secondary preventative medications after stroke is common and is associated with poor outcomes. Numerous strategies exist to promote adherence. We performed a systematic review and meta-analysis to describe the efficacy of strategies to improve adherence to stroke secondary prevention. Methods: We created a sensitive search strategy and searched multiple electronic databases (MEDLINE, EMBASE, CINAHL, PsycINFO, CENTRAL, and Web of Knowledge) for studies of interventions that aimed to enhance adherence to secondary preventative medication after stroke. We assessed quality of included studies using the Cochrane tool for assessing risk of bias. We performed narrative review and performed meta-analysis where data allowed. Results: From 12,237 titles, we included seventeen studies in our review. Eleven studies were considered to have high risk of bias, 3 with unclear risk, and 3 of low risk. Meta-analysis of available data suggested that these interventions improved adherence to individual medication classes (blood pressure-lowering drugs – OR, 2.21; 95% CI (1.63, 2.98), [P < 0.001], lipid-lowering drugs – OR, 2.11; 95% CI (1.00, 4.46), [P = 0.049], and antithrombotic drugs – OR, 2.32; 95% CI (1.18, 4.56, [P = 0.014]) but did not improve adherence to an overall secondary preventative medication regimen (OR, 1.96; 95% CI (0.50, 7.67), [P = 0.332]). Conclusion: Interventions can lead to improvement in adherence to secondary preventative medication after stroke. However, existing data is limited as several interventions, duration of follow-up, and various definitions were used. These findings need to be interpreted with caution

The Relationship between CD27 Negative and Positive B Cell Populations in Human Peripheral Blood

CD27 expression has been used to distinguish between memory and naive B cells in humans. However, low levels of mutated and isotype-switched CD27−IgD− cells are seen in healthy adults, and these are increased in some autoimmune diseases and in the elderly. Thus CD27 is not a universal marker of memory B cells in humans. Various hypotheses have been put forward as to the function of the CD27− memory population. Since we have previously found high-throughput IGHV repertoire analysis useful to distinguish “innate-like” memory B cells (CD27+IgD+), we have employed similar analyses to elucidate the relationship between CD27− and CD27+ memory B cells. IgM+IgD− memory cells in both the CD27+ and CD27− compartments share the unique characteristics of the “innate-like” IgM+IgD+CD27+ cells. The switched CD27+ and CD27− memory cells share a similar IGHV repertoire, having more in common with each other than with “innate-like” memory cells, although it is interesting that IgG2 and IgA2 subclasses of antibody in both switched memory populations have a more “innate-like” repertoire. Clonality analysis shows evidence of a close clonal relationship between the two populations in that both CD27− and CD27+ switched memory cells can be found in the same genealogical tree. The expression of CD27 does not appear to occur in a linear developmental fashion, since we see CD27− cells as precursors of CD27+ cells and vice versa. Despite the similarities, the CDR-H3 repertoire of the CD27− cells is significantly different from both the CD27+IgD+ and CD27+IgD− populations, indicating that perhaps the lack of CD27 might be related to binding properties of the Ig CDR-H3 region

Lineage tree analysis of immunoglobulin variable-region gene mutations in autoimmune diseases: chronic activation, normal selection

Autoimmune diseases show high diversity in the affected organs, clinical manifestations and disease dynamics. Yet they all share common features, such as the ectopic germinal centers found in many affected tissues. Lineage trees depict the diversification, via somatic hypermutation (SHM), of immunoglobulin variable-region (IGV) genes. We previously developed an algorithm for quantifying the graphical properties of IGV gene lineage trees, allowing evaluation of the dynamical interplay between SHM and antigen-driven selection in different lymphoid tissues, species, and disease situations. Here, we apply this method to ectopic GC B cell clones from patients with Myasthenia Gravis, Rheumatoid Arthritis, and Sjögren’s Syndrome, using data scaling to minimize the effects of the large variability due to methodological differences between groups. Autoimmune trees were found to be significantly larger relative to normal controls. In contrast, comparison of the measurements for tree branching indicated that similar selection pressure operates on autoimmune and normal control clones

The Dynamics of Germinal Centre Selection as Measured by Graph-Theoretical Analysis of Mutational Lineage Trees

We have developed a rigorous graph-theoretical algorithm for quantifying the shape properties of mutational lineage trees. We show that information about the dynamics of hypermutation and antigen-driven clonal selection during the humoral immune response is contained in the shape of mutational lineage trees deduced from the responding clones. Age and tissue related differences in the selection process can be studied using this method. Thus, tree shape analysis can be used as a means of elucidating humoral immune response dynamics in various situations

Inferring processes underlying B-cell repertoire diversity

We quantify the VDJ recombination and somatic hypermutation processes in human B-cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains. Our analysis captures the statistical properties of the naive repertoire, first after its initial generation via VDJ recombination and then after selection for functionality. We also infer statistical properties of the somatic hypermutation machinery (exclusive of subsequent effects of selection). Our main results are the following: the B-cell repertoire is substantially more diverse than T-cell repertoires, due to longer junctional insertions; sequences that pass initial selection are distinguished by having a higher probability of being generated in a VDJ recombination event; somatic hypermutations have a non-uniform distribution along the V gene that is well explained by an independent site model for the sequence context around the hypermutation site.Comment: acknowledgement adde

B-cell diversity decreases in old age and is correlated with poor health status

Older people suffer from a decline in immune system, which affects their ability to respond to infections and to raise efficient responses to vaccines. Effective and specific antibodies in responses from older individuals are decreased in favour of non-specific antibody production. We investigated the B-cell repertoire in DNA samples from peripheral blood of individuals aged 86–94 years, and a control group aged 19–54 years, using spectratype analysis of the IGHV complementarity determining region (CDR)3. We found that a proportion of older individuals had a dramatic collapse in their B-cell repertoire diversity. Sequencing of polymerase chain reaction products from a selection of samples indicated that this loss of diversity was characterized by clonal expansions of B cells in vivo. Statistical analysis of the spectratypes enabled objective comparisons and showed that loss of diversity correlated very strongly with the general health status of the individuals; a distorted spectratype can be used to predict frailty. Correlations with survival and vitamin B12 status were also seen. We conclude that B-cell diversity can decrease dramatically with age and may have important implications for the immune health of older people. B-cell immune frailty is also a marker of general frailty

sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data

Class-switch recombination (CSR) is an integral part of B cell maturation. Here we present sciCSR (pronounced 'scissor', single-cell inference of class-switch recombination), a computational pipeline that analyzes CSR events and dynamics of B cells from single-cell RNA sequencing (scRNA-seq) experiments. Validated on both simulated and real data, sciCSR re-analyzes scRNA-seq alignments to differentiate productive heavy-chain immunoglobulin transcripts from germline 'sterile' transcripts. From a snapshot of B cell scRNA-seq data, a Markov state model is built to infer the dynamics and direction of CSR. Applying sciCSR on severe acute respiratory syndrome coronavirus 2 vaccination time-course scRNA-seq data, we observe that sciCSR predicts, using data from an earlier time point in the collected time-course, the isotype distribution of B cell receptor repertoires of subsequent time points with high accuracy (cosine similarity ~0.9). Using processes specific to B cells, sciCSR identifies transitions that are often missed by conventional RNA velocity analyses and can reveal insights into the dynamics of B cell CSR during immune response

B cell immunosenescence: different features of naive and memory B cells in elderly

Elderly people show a reduced protection against new infections and a decreased response to vaccines as a consequence of impairment of both cellular and humoral immunity. In this paper we have studied memory/na\uefve B cells in the elderly, evaluating surface immunoglobulin expression, production of the pro- and anti-inflammatory cytokines, tumor necrosis factor (TNF)-\u3b1 and interleukin (IL)-10, and presence of somatic hypermutation, focusing on the IgG(+)IgD(-)CD27(-) double negative (DN) B cells that are expanded in the elderly. Our results show that na\uefve B cells from young donors need a sufficiently strong stimulus to be activated "in vitro", while na\uefve B cells from old subjects are able to produce IL-10 and TNF-\u3b1 when stimulated "physiologically" (\u3b1-CD40/IL-4), suggesting that these cells might play a role in the control of the immuno-inflammatory environment in the elderly. In addition, in the elderly there is an accumulation of DN B cells with a reduced rate of somatic hypermutation. Thus, DN B lymphocytes may be exhausted cells that are expanded and accumulate as a by-product of persistent stimulation or impaired germinal center formatio

Inflammation-induced IgE promotes epithelial hyperplasia and tumour growth

IgE is the least abundant circulating antibody class but is constitutively present in healthy tissues bound to resident cells via its high-affinity receptor, FcεRI. The physiological role of endogenous IgE antibodies is unclear but it has been suggested that they provide host protection against a variety of noxious environmental substances and parasitic infections at epithelial barrier surfaces. Here we show, in mice, that skin inflammation enhances levels of IgE antibodies that have natural specificities and a repertoire, VDJ rearrangements and CDRH3 characteristics similar to those of IgE antibodies in healthy tissue. IgE-bearing basophils are recruited to inflamed skin via CXCL12 and thymic stromal lymphopoietin (TSLP)/IL-3-dependent upregulation of CXCR4. In the inflamed skin, IgE/FcεRI-signalling in basophils promotes epithelial cell growth and differentiation, partly through histamine engagement of H1R and H4R. Furthermore, this IgE response strongly drives tumour outgrowth of epithelial cells harbouring oncogenic mutation. These findings indicate that natural IgE antibodies support skin barrier defences, but that during chronic tissue inflammation this role may be subverted to promote tumour growth