scholarly journals A multi-objective based clustering for identifying clonally-related sequences from high-throughput B cell repertoire data

2021 ◽  
Author(s):  
Nika Abdollahi ◽  
Anne Langlois De Septenville ◽  
Hugues Ripoche ◽  
Frederic Davi ◽  
Juliana Silva Bernardes

The adaptive B cell response is driven by the expansion, somatic hypermutation, and selection of B cell clones. A high number of clones in a B cell population indicates a highly diverse repertoire, while clonal size distribution and sequence diversity within clones can be related to antigen's selective pressure. Identifying clones is fundamental to many repertoire studies, including repertoire comparisons, clonal tracking and statistical analysis. Several methods have been developed to group sequences from high-throughput B cell repertoire data. Current methods use clustering algorithms to group clonally-related sequences based on their similarities or distances. Such approaches create groups by optimizing a single objective that typically minimizes intra-clonal distances. However, optimizing several objective functions can be advantageous and boost the algorithm convergence rate. Here we propose a new method based on multi-objective clustering. Our approach requires V(D)J annotations to obtain the initial clones and iteratively applies two objective functions that optimize cohesion and separation within clones simultaneously. We show that under simulations with varied mutation rates, our method greatly improves clonal grouping as compared to other tools. When applied to experimental repertoires generated from high-throughput sequencing, its clustering results are comparable to the most performing tools. The method based on multi-objective clustering can accurately identify clone members, has fewer parameter settings and presents the lowest running time among existing tools. All these features constitute an attractive option for repertoire analysis, particularly in the clinical context to unravel the mechanisms involved in the development and evolution of B cell malignancies.

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Marie Ghraichy ◽  
Valentin von Niederhäusern ◽  
Aleksandr Kovaltsuk ◽  
Jacob D Galson ◽  
Charlotte M Deane ◽  
...  

Several human B-cell subpopulations are recognized in the peripheral blood, which play distinct roles in the humoral immune response. These cells undergo developmental and maturational changes involving VDJ recombination, somatic hypermutation and class switch recombination, altogether shaping their immunoglobulin heavy chain (IgH) repertoire. Here, we sequenced the IgH repertoire of naïve, marginal zone, switched and plasma cells from 10 healthy adults along with matched unsorted and in silico separated CD19+ bulk B cells. Using advanced bioinformatic analysis and machine learning, we show that sorted B cell subpopulations are characterised by distinct repertoire characteristics on both the individual sequence and the repertoire level. Sorted subpopulations shared similar repertoire characteristics with their corresponding in silico separated subsets. Furthermore, certain IgH repertoire characteristics correlated with the position of the constant region on the IgH locus. Overall, this study provides unprecedented insight over mechanisms of B cell repertoire control in peripherally circulating B cell subpopulations.


2015 ◽  
Vol 370 (1676) ◽  
pp. 20140243 ◽  
Author(s):  
Yuval Elhanati ◽  
Zachary Sethna ◽  
Quentin Marcou ◽  
Curtis G. Callan ◽  
Thierry Mora ◽  
...  

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, owing 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.


2017 ◽  
Vol 214 (7) ◽  
pp. 1991-2003 ◽  
Author(s):  
Jean-Nicolas Schickel ◽  
Salomé Glauzy ◽  
Yen-Shing Ng ◽  
Nicolas Chamberlain ◽  
Christopher Massad ◽  
...  

The germline immunoglobulin (Ig) variable heavy chain 4–34 (VH4-34) gene segment encodes in humans intrinsically self-reactive antibodies that recognize I/i carbohydrates expressed by erythrocytes with a specific motif in their framework region 1 (FWR1). VH4-34–expressing clones are common in the naive B cell repertoire but are rarely found in IgG memory B cells from healthy individuals. In contrast, CD27+IgG+ B cells from patients genetically deficient for IRAK4 or MYD88, which mediate the function of Toll-like receptors (TLRs) except TLR3, contained VH4-34–expressing clones and showed decreased somatic hypermutation frequencies. In addition, VH4-34–encoded IgGs from IRAK4- and MYD88-deficient patients often displayed an unmutated FWR1 motif, revealing that these antibodies still recognize I/i antigens, whereas their healthy donor counterparts harbored FWR1 mutations abolishing self-reactivity. However, this paradoxical self-reactivity correlated with these VH4-34–encoded IgG clones binding commensal bacteria antigens. Hence, B cells expressing germline-encoded self-reactive VH4-34 antibodies may represent an innate-like B cell population specialized in the containment of commensal bacteria when gut barriers are breached.


2015 ◽  
Author(s):  
Yuval Elhanati ◽  
Zachary Sethna ◽  
Quentin Marcou ◽  
Curtis G Callan ◽  
Thierry Mora ◽  
...  

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.


2019 ◽  
Author(s):  
Natasha D. Durham ◽  
Aditi Agrawal ◽  
Eric Waltari ◽  
Derek Croote ◽  
Fabio Zanini ◽  
...  

AbstractEliciting broadly neutralizing antibodies (bNAbs) against the four dengue virus serotypes (DENV1-4) that are spreading into new territories is an important goal of vaccine design. To delineate bNAb targets, we characterized 28 monoclonal antibodies belonging to expanded and hypermutated clonal families identified by transcriptomic analysis of single plasmablasts from DENV-infected individuals. Among these, we identified two somatically related bNAbs that potently neutralized DENV1-4. Mutagenesis studies revealed that the major recognition determinants of these bNAbs are in E protein domain I, distinct from the only known class of human bNAbs against flaviviruses with a well-defined epitope. B cell repertoire analysis from acute-phase peripheral blood suggested a memory origin and divergent somatic hypermutation pathways for these bNAbs, and a limited number of mutations was sufficient for neutralizing activity. Our study suggests multiple B cell evolutionary pathways leading to DENV bNAbs targeting a novel epitope that can be exploited for vaccine design.


2021 ◽  
Author(s):  
Marie Ghraichy ◽  
Valentin von Niederhäusern ◽  
Aleksandr Kovaltsuk ◽  
Jacob Daniel Galson ◽  
Charlotte M Deane ◽  
...  

Background: Several human B-cell subpopulations are recognized in the peripheral blood, which play distinct roles in the humoral immune response. These cells undergo developmental and maturational changes involving VDJ recombination, somatic hypermutation and class switch recombination, altogether shaping their immunoglobulin heavy chain (IgH) repertoire. Methods: Here, we sequenced the IgH repertoire of naïve, marginal zone, switched and plasma cells from 10 healthy adults along with matched unsorted and in silico separated CD19+ bulk B cells. We used advanced bioinformatic analysis and machine learning to thoroughly examine and compare these repertoires. Results: We show that sorted B cell subpopulations are characterised by distinct repertoire characteristics on both the individual sequence and the repertoire level. Sorted subpopulations shared similar repertoire characteristics with their corresponding in silico separated subsets. Furthermore, certain IgH repertoire characteristics correlated with the position of the constant region on the IgH locus. Conclusion: Overall, this study provides unprecedented insight over mechanisms of B cell repertoire control in peripherally circulating B cell subpopulations.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3132-3132
Author(s):  
Dimitrios Papaioannou ◽  
Anna-Maria Strothmeyer ◽  
Marcus Dühren-von Minden ◽  
Marcelo A. Navarrete ◽  
Katja Zirlik ◽  
...  

Abstract Abstract 3132 The idiotype (Id) of malignant lymphomas is a tumor-specific antigen and has been evaluated for active immunotherapy predominantly in follicular lymphoma (FL). We have previously described “reverse immunology” evidence that HLA class I-dependent and hence presumably T-cell mediated selection pressure restricts the growth of malignant FL clones with comparatively highly immunogenic Ids (Strothmeyer et al., Blood, epub 2010). This effect was mostly attributable to the Id CDRs. We therefore hypothesized that somatic hypermutation, a constitutively active process in FL, is the mechanism that creates immunogenic Id epitopes and enables T-cell mediated immunosurveillance. To test this hypothesis, we analyzed Id of FL that utilized the same Vh gene but arose in individuals with different HLA types (IGHV3-23*01, n=9 patients: IGHV3-7*01, n=3). For every represented HLA type, an “immunogenicity landscape” mapping was performed by plotting the ten most immunogenic peptides of the germ-line Vh sequence in comparison to FL Id peptides in the order of their HLA binding strength as predicted by the BIMAS algorithm for the respective patient. Neither changes in the order of peptides nor major differences in their binding scores were observed. Parallel plotting of Vh-related Ids from different HLA types revealed novel peptides with higher binding scores within and in addition to the ten highest ranking epitopes (Figures). Comparisons of these peptides with the germ-line and the index patient's sequence directly demonstrated that somatic hypermutation creates peptides that would have strongly bound to HLA type of the index patient but were immunologically neutral in the patient of origin. Occurrence of such highly immunogenic peptides by somatic hypermutation would hence not be tolerated by an FL patient's immune system. To explore whether this mechanism also operates in other lymphoma types, we analyzed predicted HLA-binding Id peptides from mantle cell (n=20) and marginal zone (n=12) lymphomas. Like in FL, the median sum of the 20 peptides with the highest BIMAS scores were to various degrees less immunogenic on the autologous HLA type than on allogeneic HLA types (ratio of autologous to allogeneic BIMAS sum scores: FL: 0.63; MCL: 0.78; MZL: 0.87). In subanalyses of the CDR, these differences were observed only in FL and MCL but not in MZL (CDR1: FL 0.40, MCL 0.55. MZL 1.39; CDR2: FL 0.25, MCL 0.36; MZL 1.54: CDR3: FL 0.43, MCL 0.53, MZL 1.28). To investigate whether HLA-dependent immunosurveillance acts on normal B-cell receptors, we compared BIMAS sum scores of 96 non-clonal Ids present in diagnostic biopsies of 29 FL and MCL patients. These Ids represent bona fide contaminating, healthy B cells. No significant differential immunogenicity existed for the entire Vh sequences or individual CDR regions, regardless of their mutational status. We therefore randomly sequenced B-cell receptors from two mouse strains with an identical B6 genetic background but a congenic H-2 complex (C57BL/6ByJ: H-2b; 422 sequences; B6-H2d/bByJ: H-2d; 412 sequences). In these SPF-bred mice, 61% and 71% of sequences, respectively, were unmutated. Significantly higher immunogenicity was observed in the FR1-3 regions of C57BL/6ByJ compared to B6-H2d/bByJ Ids on H-2kd (p=0.04). Also, several Vh genes were significantly (Fisher's exact test) less frequent in mice expressing the MHC type with stronger binding to Id-derived peptides of the corresponding germ-line Vh sequence. Overall, the ratio of predicted MHC binding strength of the 20 highest scoring peptides from 59 represented germ-line Vh genes correlated to the relative frequency of representation of these genes in the peripheral B-cell repertoire (p=0.016, Pearson correlation). Collectively, these results indicate that somatic hypermutation is the predominant mechanism that enables T-cell mediated control of malignant B-cell clones in FL but possibly also MCL on the basis of the HLA binding of Id-derived peptides. In addition, HLA binding strength of germ-line-encoded Vh peptides appears to exert a subtle modulation of the primary B cell repertoire by MHC class I-restricted T cells. These findings strengthen the theoretical basis of active Id-directed immunotherapy of B-cell lymphomas with mutated antigen receptors. In addition, they may also lead to a novel explanation for the association of HLA type with aberrant functions of the nonmalignant immune system. Disclosures: No relevant conflicts of interest to declare.


2019 ◽  
Vol 20 (2) ◽  
pp. 417 ◽  
Author(s):  
Soohyun Kim ◽  
Hyunho Lee ◽  
Jinsung Noh ◽  
Yonghee Lee ◽  
Haejun Han ◽  
...  

: YYB-101 is a humanized rabbit anti-human hepatocyte growth factor (HGF)-neutralizing antibody currently in clinical trial. To test the effect of HGF neutralization with antibody on anti-cancer T cell immunity, we generated surrogate antibodies that are reactive to the mouse homologue of the epitope targeted by YYB-101. First, we immunized a chicken with human HGF and monitored changes in the B cell repertoire by next-generation sequencing (NGS). We then extracted the VH gene repertoire from the NGS data, clustered it into components by sequence homology, and classified the components by the change in the number of unique VH sequences and the frequencies of the VH sequences within each component following immunization. Those changes should accompany the preferential proliferation and somatic hypermutation or gene conversion of B cells encoding HGF-reactive antibodies. One component showed significant increases in the number and frequencies of unique VH sequences and harbored genes encoding antibodies that were reactive to human HGF and competitive with YYB-101 for HGF binding. Some of the antibodies also reacted to mouse HGF. The selected VH sequences shared 98.3% identity and 98.9% amino acid similarity. It is therefore likely that the antibodies encoded by them all react to the epitope targeted by YYB-101.


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