Martin V, Wu Y-C, Kipling D, Dunn-Walters D (2015) Ageing of the B-cell repertoire, Philosophical Transactions of the Royal Society B 370 (1676)
The Royal Society Publishing
Older people are more susceptible to infection, less responsive to vaccination and have a more inflammatory immune environment. Using spectratype analysis, we have previously shown that the B-cell repertoire of older people shows evidence of inappropriate clonal expansions in the absence of challenge, and that this loss of B-cell diversity correlates with poor health. Studies on response to vaccination, using both spectratyping and high-throughput sequencing of the repertoire, indicate that older responses to challenge are lacking in magnitude and/or delayed significantly. Also that some of the biologically significant differences may be in different classes of antibody. We have also previously shown that normal young B-cell repertoires can vary between different phenotypic subsets of B cells. In this paper, we present an analysis of immunoglobulin repertoire in different subclasses of antibody in five different populations of B cell, and show how the repertoire in these different groups changes with age. Although some age-related repertoire differences occur in naive cells, before exogenous antigen exposure, we see indications that there is a general dysregulation of the selective forces that shape memory B-cell populations in older people.
Bagnara D, Squillario M, Kipling D, Mora T, Walczak AM, Da Silva L, Weller S, Dunn-Walters D, Weill J-C, Reynaud C-A (2015) A reassessment of IgM memory subsets in humans, Journal of Immunology 195 (8) pp. 3716-3724
American Association of Immunologists
From paired blood and spleen samples from three adult donors, we performed high-throughput VH sequencing of human B cell subsets defined by IgD and CD27 expression: IgD+CD27+ (?marginal zone [MZ]?), IgD?CD27+ (?memory,? including IgM [?IgM-only?], IgG and IgA) and IgD?CD27? cells (?double-negative,? including IgM, IgG, and IgA). A total of 91,294 unique sequences clustered in 42,670 clones, revealing major clonal expansions in each of these subsets. Among these clones, we further analyzed those shared sequences from different subsets or tissues for VH gene mutation, H-CDR3-length, and VH/JH usage, comparing these different characteristics with all sequences from their subset of origin for which these parameters constitute a distinct signature. The IgM-only repertoire profile differed notably from that of MZ B cells by a higher mutation frequency and lower VH4 and higher JH6 gene usage. Strikingly, IgM sequences from clones shared between the MZ and the memory IgG/IgA compartments showed a mutation and repertoire profile of IgM-only and not of MZ B cells. Similarly, all IgM clonal relationships (among MZ, IgM-only, and double-negative compartments) involved sequences with the characteristics of IgM-only B cells. Finally, clonal relationships between tissues suggested distinct recirculation characteristics between MZ and switched B cells. The ?IgM-only? subset (including cells with its repertoire signature but higher IgD or lower CD27 expression levels) thus appear as the only subset showing precursor?product relationships with CD27+ switched memory B cells, indicating that they represent germinal center?derived IgM memory B cells and that IgM memory and MZ B cells constitute two distinct entities.
Tete SM, Kipling D, Westra J, de Haan A, Bijl M, Dunn-Walters D, Sahota SS, Bos NA (2015) Monoclonal paraprotein influences baseline B-cell repertoire diversity and perturbates influenza vaccination-induced B-cell response, Experimental Hematology 43 (6) pp. 439-447 Elsevier
Monoclonal gammopathy of undetermined significance (MGUS) arises from a clonal expansion
of plasma cells in the bone marrow, secreting monoclonal (M) paraprotein. It is associated
with increased susceptibility to infections, which may reflect altered B-cell repertoire.
To investigate this, we examined the immunoglobulin (Ig) M, IgG, and IgA B-cell repertoire
diversity in MGUS at baseline and after influenza vaccination (n [ 16) in comparison with
healthy controls (HCs; n [ 16). The Complementary Determining Region 3 region of the
immunoglobulin heavy chain variable region gene was amplified and B-cell spectratypes
analyzed by high-resolution electrophoresis. Spectratype Gaussian distribution, kurtosis,
and skewness were quantified to measure repertoire shifts. Both HC and MGUS baseline spectratypes
show interindividual variability that is more pronounced in the IGHG and IGHA repertoires.
Overall, baseline B-cell repertoire is more altered in MGUS, with oligoclonality
observed in 50% (p [ 0.01). Postvaccination, significant differences emerged in MGUS in
relation to M-protein levels. High M-protein concentration is associated with a more oligoclonal
IgG and IgA response at day 7 postvaccination, and, in contrast to HCs, vaccination also
induced significant perturbations in the MGUS IgM repertoire at day 7 (p [ 0.005). Monoclonal
expansion in MGUS thus has an effect on the baseline B-cell repertoire and influences
the recruited repertoire upon vaccination.
Fraser LD, Zhao Y, Lutalo PMK, D?Cruz DP, Cason J, Silva JS, Dunn-Walters D, Nayar S, Cope AP, Spencer J (2016) Immunoglobulin light chain allelic inclusion in systemic lupus erythematosus, European Journal of Immunology 45 (8) pp. 2409-2419 Wiley
The principles of allelic exclusion state that each B cell expresses a single light and heavy chain pair. Here, we show that B cells with both kappa and lambda light chains (Igº and Ig») are enriched in some patients with the systemic autoimmune disease systemic lupus erythematosus (SLE), but not in the systemic autoimmune disease control granulomatosis with polyangiitis. Detection of dual Igº and Ig» expression by flow cytometry could not be abolished by acid washing or by DNAse treatment to remove any bound polyclonal antibody or complexes, and was retained after two days in culture. Both surface and intracytoplasmic dual light chain expression was evident by flow cytometry and confocal microscopy. We observed reduced frequency of rearrangements of the kappa-deleting element (KDE) in SLE and an inverse correlation between the frequency of KDE rearrangement and the frequency of dual light chain expressing B cells. We propose that dual expression of Igº and Ig» by a single B cell may occur in some patients with SLE when this may be a consequence of reduced activity of the KDE.
Tabibian-Keissar? H, Hazanov L, Schiby G, Rosenthal N, Rakovsky A, Michaeli M, Shahaf GL, Pickman Y, Rosenblatt K, Melamed D, Dunn-Walters D, Mehr R, Barshack I (2015) Aging affects B-cell antigen receptor repertoire diversity in primary and secondary lymphoid tissues, European Journal of Immunology 46 (2) pp. 480-492 2015 WILEY-VCH Verlag GmbH & Co
The elderly immune system is characterized by reduced responses to infections and vaccines,
and an increase in the incidence of autoimmune diseases and cancer. Age-related
deficits in the immune system may be caused by peripheral homeostatic pressures that
limit bone marrow B-cell production or migration to the peripheral lymphoid tissues.
Studies of peripheral blood B-cell receptor spectratypes have shown that those of the
elderly are characterized by reduced diversity, which is correlated with poor health status.
In the present study, we performed for the first time high-throughput sequencing
of immunoglobulin genes from archived biopsy samples of primary and secondary lymphoid
tissues in old (74 ± 7 years old, range 61?89) versus young (24 ± 5 years old,
range 18?45) individuals, analyzed repertoire diversities and compared these to results
in peripheral blood. We found reduced repertoire diversity in peripheral blood and lymph
node repertoires from old people, while in the old spleen samples the diversity was larger
than in the young. There were no differences in somatic hypermutation characteristics
between age groups. These results support the hypothesis that age-related immune
frailty stems from altered B-cell homeostasis leading to narrower memory B-cell repertoires,
rather than changes in somatic hypermutation mechanisms.
Wu Y-C, Kipling D, Dunn-Walters D (2015) Assessment of B cell repertoire in humans, Methods in Molecular Biology 1343 pp. 199-218 Humana Press
The B cell receptor (BCR) repertoire is highly diverse. Repertoire diversity is achieved centrally by somatic recombination of immunoglobulin (Ig) genes and peripherally by somatic hypermutation and Ig heavy chain class-switching. Throughout these processes, there is selection for functional gene rearrangements, selection against gene combinations resulting in self-reactive BCRs, and selection for BCRs with high affinity for exogenous antigens after challenge. Hence, investigation of BCR repertoires from different groups of B cells can provide information on stages of B cell development and shed light on the etiology of B cell pathologies. In most instances, the third complementarity determining region of the Ig heavy chain (CDR-H3) contributes the majority of amino acids to the antibody/antigen binding interface. Although CDR-H3 spectratype analysis provides information on the overall diversity of BCR repertoires, this fairly simple technique analyzes the relative quantities of CDR-H3 regions of each size, within a range of approximately 10?80 bp, without sequence detail and thus is limited in scope. High-throughput sequencing (HTS) techniques on the Roche 454 GS FLX Titanium system, however, can generate a wide coverage of Ig sequences to provide more qualitative data such as V, D, and J usage as well as detailed CDR3 sequence information. Here we present protocols in detail for CDR-H3 spectratype analysis and HTS of human BCR repertoires.
Sabouria Z, Schofield P, Horikawa K, Spierings E, Kipling D, Randall KL, Langley D, Roome B, Vazquez-Lombardi R, Rouet R, Hermes J, Chan TD, Brink R, Dunn-Walters D, Christ D, Goodnow CC (2014) Redemption of autoantibodies on anergic B cells by variable-region glycosylation and mutation away from self-reactivity, PNAS 111 (25) pp. E2567-E2575
National Academy of Sciences
The best-understood mechanisms for achieving antibody self/nonself
discrimination discard self-reactive antibodies before they can
be tested for binding microbial antigens, potentially creating holes
in the repertoire. Here we provide evidence for a complementary
mechanism: retaining autoantibodies in the repertoire displayed
as low levels of IgM and high IgD on anergic B cells, masking a
varying proportion of autoantibody-binding sites with carbohydrates,
and removing their self-reactivity by somatic hypermutation
and selection in germinal centers (GCs). Analysis of human
antibody sequences by deep sequencing of isotype-switched
memory B cells or in IgG antibodies elicited against allogeneic
RhD+ erythrocytes, vaccinia virus, rotavirus, or tetanus toxoid provides
evidence for reactivation of anergic IgMlow IgD+ IGHV4-34+
B cells and removal of cold agglutinin self-reactivity by hypermutation,
often accompanied by mutations that inactivated an
N-linked glycosylation sequon in complementarity-determining region
2 (CDR2). In a Hy10 antibody transgenic model where anergic
B cells respond to a biophysically defined lysozyme epitope displayed
on both foreign and self-antigens, cell transfers revealed
that anergic IgMlow IgD+ B cells form twice as many GC progeny
as naïve IgMhi IgD+ counterparts. Their GC progeny were rapidly
selected for CDR2 mutations that blocked 72% of antigen-binding
sites with N-linked glycan, decreased affinity 100-fold, and then
cleared the binding sites of blocking glycan. These results provide
evidence for a mechanism to acquire self/non-self discrimination
by somatic mutation away from self-reactivity, and reveal how
varying the efficiency of N-glycosylation provides a mechanism
to modulate antibody avidity.
Michaeli M, Tabibian-Keissar H, Schiby G, Shahaf G, Pickman Y, Hazanov L, Rosenblatt K, Dunn-Walters D, Barshack I, Mehr R (2014) Immunoglobulin gene repertoire diversification and selection in the stomach ? from gastritis to gastric lymphomas, Frontiers in Immunology 5 264 pp. 1-14 Frontiers Media
Chronic gastritis is characterized by gastric mucosal inflammation due to autoimmune
responses or infection, frequently with Helicobacter pylori. Gastritis with H. pylori background
can cause gastric mucosa-associated lymphoid tissue lymphoma (MALT-L), which
sometimes further transforms into diffuse large B-cell lymphoma (DLBCL). However, gastric
DLBCL can also be initiated de novo. The mechanisms underlying transformation into
DLBCL are not completely understood.We analyzed immunoglobulin repertoires and clonal
trees to investigate whether and how immunoglobulin gene repertoires, clonal diversification,
and selection in gastritis, gastric MALT-L, and DLBCL differ from each other and from
normal responses. The two gastritis types (positive or negative for H. pylori) had similarly
diverse repertoires. MALT-L dominant clones (defined as the largest clones in each sample)
presented higher diversification and longer mutational histories compared with all other
conditions. DLBCL dominant clones displayed lower clonal diversification, suggesting the
transforming events are triggered by similar responses in different patients. These results
are surprising, as we expected to find similarities between the dominant clones of gastritis
and MALT-L and between those of MALT-L and DLBCL.
The CD27+IgD+ B cell population, known as IgM memory, reduces with age. It is thought that this population is
responsible for pneumococcal polysaccharide T-independent responses, and that the age-related reduction might be
partially responsible for the increased susceptibility of older people to bacterial pathogens. There are other IgM+ B cell
populations that do not express IgD. We compared the different IgM populations using high-throughput sequencing
of the immunoglobulin (Ig) gene repertoire and multidimensional cell phenotyping and found that the different
populations of IgM cells, defined by CD27 and IgD expression, have repertoire differences. Some of these differences
are likely indicative of different selection pressures in an immune response, although the older individuals were
found to have a changed repertoire in naive B cells, which may contribute to some of the changes seen in memory
cells. In addition, even within the CD27+IgD+ IgM memory population there are multiple cell types. We show
that the level of IgM expression varies substantially and hypothesize that this distinguishes between T-dependent
and T-independent types of IgM memory cells. Significant age-related changes in the relative proportions of these
populations may exacerbate the reduction in T-independent responders in old age.
Dunn-Walters D (2015) The ageing human B cell repertoire: A failure of selection?, Clinical & Experimental Immunology 183 (1) pp. 50-56 Wiley
B cells undergo a number of different developmental stages, from initial formation of their B cell receptor (BCR) genes to differentiation into antibody-secreting plasma cells. Because the BCR is vital in these differentiation steps, autoreactive and exogenous antigen binding to the BCR exert critical selection pressures to shape the B cell repertoire. Older people are more prone to infectious disease, less able to respond well to vaccination and more likely to have autoreactive antibodies. Here we review evidence of changes in B cell repertoires in older people, which may be a reflection of age-related changes in B cell selection processes.
Björkman A, Du L, van der Burg M, Cormier-Daire V, Borck G, Pié J, Anderlid B, Hammarström L, Ström L, de Villartay J, Kipling D, Dunn-Walters D, Pan-Hammarström Q (2017) Reduced immunoglobulin gene diversity in patients with Cornelia de Lange syndrome, Journal of Allergy and Clinical Immunology 141 (1) pp. 408-411.e8
B cells rely on a broad receptor repertoire to provide protection against a wide range of pathogens. This is in part achieved through V(D)J recombination, which, by assembling various combinations of variable (V), diversity (D), and joining (J) genes, creates different IgV regions.1 The recombination processes is initiated by recombination-activating gene (RAG) 1/RAG2 enzymes and requires a functional nonhomologous end-joining (NHEJ) machinery. B cells can further diversify their IgV regions through somatic hypermutation (SHM) to improve affinity between the antibody and antigen and switch the isotype of antibody produced by class-switch recombination (CSR).
Antibody variable regions are composed of a heavy and a light chain and in humans there are two light chain isotypes: kappa and lambda. Despite their importance in receptor editing, the light chain is often overlooked in the antibody literature, with the focus being on the heavy chain CDR-H3 region. In this paper, we set out to investigate the physicochemical and structural differences between human kappa and lambda light chain CDR regions. We constructed a dataset containing over 29,000 - light chain variable region sequences from IgM-transcribing, newly formed B cells isolated from human bone marrow and peripheral blood. We also used a published human naïve dataset to investigate the CDR-H3 properties of heavy chains paired with kappa and lambda light chains, and probed the Protein Data Bank (PDB) to investigate the structural differences between kappa and lambda antibody CDR regions. We found that kappa and lambda light chains have very different CDR physicochemical and structural properties, whereas the heavy chains with which they are paired do not differ significantly. We also observed that the mean CDR3 N nucleotide addition in the kappa, lambda and heavy chain gene rearrangements are correlated within donors, but can differ between donors. This indicates that TdT may work with differing efficiencies between different people, but the same efficiency in the different classes of immunoglobulin chain within one person. We have observed large differences in the physicochemical and structural properties of kappa and lambda light chain CDR regions. This may reflect different roles in the humoral immune response.
Martin V, Wu Y, Townsend C, Lu G, O'Hare J, Mozeika A, Coolen A, Kipling D, Fraternali F, Dunn-Walters D (2016) Transitional B cells in early human B cell development - time to revisit the paradigm?, Frontiers in Immunology 7 546
The B cell repertoire is generated in the adult bone marrow by an ordered series of gene rearrangement processes that result in massive diversity of immunoglobulin (Ig) genes, and consequently an equally large number of potential specificities for antigen. As the process is essentially random, then cells exhibiting excess reactivity with self-antigens are generated and need to be removed from the repertoire before the cells are fully mature. Some of the cells are deleted, and some will undergo receptor editing to see if changing the light chain can rescue an autoreactive antibody. As a consequence, the binding properties of the B cell receptor are changed as development progresses through pre- B>>immature>>transitional>>naïve phenotypes. Using long-read, high-throughput, sequencing we have produced a unique set of sequences from these four cell types in human bone marrow and matched peripheral blood and our results describe the effects of tolerance selection on the B cell repertoire at the Ig gene level. Most strong effects of selection are seen within the heavy chain repertoire, and can be seen both in gene usage and in CDR-H3 characteristics. Age-related changes are small and only the size of the CDR-H3 shows constant and significant change in these data. The paucity of significant changes in either kappa or lambda light chain repertoires implies that either the heavy chain has more influence over autoreactivity than light chain and/or that switching between kappa and lambda light chains, as opposed to switching within the light chain loci, may effect a more successful autoreactive rescue by receptor editing. Our results show that the transitional cell population contains cells other than those that are part of the pre-B>>immature>>transitional>>naïve development pathway, since the population often shows a repertoire that is outside the trajectory of gene loss/gain between pre-B and naïve stages.
Human B cells produce antibodies, which bind to their cognate antigen based on distinct molecular properties of the antibody CDR loop. We have analysed a set of 10 antibodies showing a clear difference in their binding properties to a panel of antigens, resulting in two subsets of antibodies with a distinct binding phenotype. We call the observed binding multiplicity ?promiscuous? and selected physico-chemical CDRH3 characteristics and conformational preferences may characterise these promiscuous antibodies. To classify CDRH3 physico-chemical properties playing a role in their binding properties, we used statistical analyses of the sequences annotated by Kidera factors. To characterise structure-function requirements for antigen binding multiplicity we employed Molecular Modelling and Monte Carlo based coarse-grained simulations. The ability to predict the molecular causes of promiscuous, multi-binding behaviour would greatly improve the efficiency of the therapeutic antibody discovery process.
Moody S, Escudero-Ibarz L, Wang M, Clipson A, Ochoa Ruiz E, Dunn-Walters D, Xue X, Zeng N, Robson A, Chuang S, Cogliatti S, Liu H, Goodlad J, Ashton-Key M, Raderer M, Bi Y, Du M (2017) Significant association between TNFAIP3 inactivation and biased IGHV4-34 usage in MALT lymphoma, Journal of Pathology 243 (1) pp. 3-8
Both antigenic drive and genetic change play a critical role in the development of MALT lymphoma, but neither alone is sufficient for malignant transformation, and lymphoma development critically depends on their cooperation. However, which of these different events concur and how they cooperate in MALT lymphomagenesis is totally unknown. To explore this, we investigated somatic mutations of 17 genes and IGHV usage in 179 MALT lymphomas from various sites. We showed that: 1) there was a significant association between the biased usage of IGHV4-34 (binds to the carbohydrate I/i antigens) and inactivating mutation of TNFAIP3 (encoding a global negative regulator of the canonical NF-kB pathway) in ocular adnexal MALT lymphoma; 2) IGHV1-69 was significantly overrepresented (54%) in MALT lymphoma of salivary gland, but not associated with mutation in any of the 17 genes investigated; and 3) MALT lymphoma lacked mutations frequently seen in other B-cell lymphomas characterised by constitutive NF-kB activities, including CD79B, CARD11, MYD88, TNFRSF11A and TRAF3. Our findings show for the first time a significant association between biased usage of autoreactive IGHV and somatic mutation of NF-kB regulators in MALT lymphoma, arguing for their cooperation in sustaining chronic BCR signalling and driving oncogenesis in lymphoma development.
Dunn-Walters D, O?Hare J (2017) Older Human B Cells and Antibodies, In: Fulop T, Franceschi C, Hirokawa K, Pawelec G (eds.), Handbook of Immunosenescence Handbook of Immunosenescence pp. 1-34
Springer International Publishing
B cells have a number of different roles in the immune response. Their excellent antigen presentation potential can contribute to the activation of other cells of the immune system, and evidence is emerging that specialized subsets of these cells, that may be increased with age, can influence the cell-mediated immune system in antitumor responses. They can also regulate immune responses, to avoid autoreactivity and excessive inflammation. Deficiencies in regulatory B cells may be beneficial in cancer but will only exacerbate the inflammatory environment that is a hallmark of aging. The B cell role as antibody producers is particularly important, since antibodies perform numerous different functions in different environments. Although studying tissue responses in humans is not as easy as in mice, we do know that certain classes of antibodies are more suited to protecting the mucosal tissues (IgA) or responding to T-independent bacterial polysaccharide antigens (IgG2) so we can make some inference with respect to tissue-specific immunity from a study of peripheral blood. We can also make inferences about changes in B cell development with age by looking at the repertoire of different B cell populations to see how age affects the selection events that would normally occur to avoid autoreactivity, or increase specificity, to antigen.
The immune system defends against infection, but older people paradoxically suffer not only from failing immunity resulting in increased susceptibility to infections and decreased responsiveness to vaccination, but at the same time increased inflammation and immunopathology accompanying immune responses. Interventions to reduce such deleterious effects while enhancing protective immunity are challenging but need to be confronted if we are to deal successfully with the increasing numbers of elderly and frail people in modern societies. To do this, we need to understand the mechanisms responsible for age-associated increased susceptibility to infections and immune-influenced chronic degenerative diseases of ageing. Defining relevant age-associated alterations and identifying reliable biomarkers for monitoring clinically-relevant immune status in the elderly population is crucial to overcoming these problems. Here, we briefly outline age-associated changes to immunity collectively termed ?immunosenescence?
Intestinal homeostasis relies on a continuous dialogue between the commensal bacteria and the immune system. Natural killer T (NKT) cells, which recognize CD1d-restricted microbial lipids and self-lipids, contribute to the regulation of mucosal immunity, yet the mechanisms underlying their functions remain poorly understood. Here, we demonstrate that NKT cells respond to intestinal lipids and CD11c+ cells (including dendritic cells (DCs) and macrophages) are essential to mediate lipid presentation within the gut ultimately controlling intestinal NKT cell homeostasis and activation. Conversely, CD1d and NKT cells participate in the control of the intestinal bacteria composition and compartmentalization, in the regulation of the IgA repertoire and in the induction of regulatory T cells within the gut. These changes in intestinal homeostasis require CD1d expression on DC/macrophage populations as mice with conditional deletion of CD1d on CD11c+ cells exhibit dysbiosis and altered immune homeostasis. These results unveil the importance of CD11c+ cells in controlling lipid-dependent immunity in the intestinal compartment and reveal an NKT cell?DC crosstalk as a key mechanism for the regulation of gut homeostasis.
The human immunoglobulin repertoire is a hugely diverse set of sequences that are formed by processes of gene rearrangement, heavy and light chain gene assortment, class switching and somatic hypermutation. Early B cell development produces diverse IgM and IgD B cell receptors on the B cell surface, resulting in a repertoire that can bind many foreign antigens but which has had self-reactive B cells removed. Later antigen-dependent development processes adjust the antigen affinity of the receptor by somatic hypermutation. The effector mechanism of the antibody is also adjusted, by switching the class of the antibody from IgM to one of seven other classes depending on the required function. There are many instances in human biology where positive and negative selection forces can act to shape the immunoglobulin repertoire and therefore repertoire analysis can provide useful information on infection control, vaccination efficacy, autoimmune diseases and cancer. It can also be used to identify antigen-specific sequences that may be of use in therapeutics. The juxtaposition of lymphocyte development and numerical evaluation of immune repertoires has resulted in the growth of a new sub-speciality in immunology where immunologists and computer scientists/physicists collaborate to assess immune repertoires and develop models of immune action.
Antibody repertoire analysis by high throughput sequencing
is now widely used, but a persisting challenge
is enabling immunologists to explore their data
to discover discriminating repertoire features for
their own particular investigations. Computational
methods are necessary for large-scale evaluation
of antibody properties. We have developed BRepertoire,
a suite of user-friendly web-based software
tools for large-scale statistical analyses of repertoire
data. The software is able to use data preprocessed
by IMGT, and performs statistical and comparative
analyses with versatile plotting options. BRepertoire
has been designed to operate in various modes, for
example analysing sequence-specific V(D)J gene usage,
discerning physico-chemical properties of the
CDR regions and clustering of clonotypes. Those
analyses are performed on the fly by a number of R
packages and are deployed by a shiny web platform.
The user can download the analysed data in different
table formats and save the generated plots as
image files ready for publication.We believe BRepertoire
to be a versatile analytical tool that complements
experimental studies of immune repertoires.
To illustrate the server?s functionality, we show use
cases including differential gene usage in a vaccination
dataset and analysis of CDR3H properties in
old and young individuals. The server is accessible
Crawford Greg, Hayes Mark David, Seoane Rocio Castro, Ward Sophie, Dalessandri Tim, Lai Chester, Healy Eugene, Kipling David, Proby Charlotte, Moyes Colin, Green Kile, Best Katie, Haniffa Muzlifah, Botto Marina, Dunn-Walters Deborah, Strid Jessica (2018) Epithelial damage and tissue ³´ T cells promote a unique tumor-protective IgE response, Nature Immunology 19 pp. 859-870
Nature Publishing Group
IgE is an ancient and conserved immunoglobulin isotype with potent immunological function. Nevertheless, the regulation of IgE responses remains an enigma, and evidence of a role for IgE in host defense is limited. Here we report that topical exposure to a common environmental DNA-damaging xenobiotic initiated stress surveillance by ³´TCR+ intraepithelial lymphocytes that resulted in class switching to IgE in B cells and the accumulation of autoreactive IgE. High-throughput antibody sequencing revealed that ³´ T cells shaped the IgE repertoire by supporting specific variable-diversity-joining (VDJ) rearrangements with unique characteristics of the complementarity-determining region CDRH3. This endogenous IgE response, via the IgE receptor FcµRI, provided protection against epithelial carcinogenesis, and expression of the gene encoding FcµRI in human squamous-cell carcinoma correlated with good disease prognosis. These data indicate a joint role for immunosurveillance by T cells and by B cells in epithelial tissues and suggest that IgE is part of the host defense against epithelial damage and tumor development.