scholarly journals Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data

2019 ◽  
Author(s):  
Nima Nouri ◽  
Steven H. Kleinstein
Keyword(s):  
B Cell ◽  
Spectral Clustering ◽  
Somatic Hypermutation ◽  
Cell Clone ◽  
R Package ◽  
Affinity Maturation ◽  
Distance Functions ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Adaptive Immune

AbstractMotivationAdaptive immune receptor repertoire sequencing (AIRR-Seq) offers the possibility of identifying and tracking B cell clonal expansions during adaptive immune responses. Members of a B cell clone are descended from a common ancestor and share the same initial V(D)J rearrangement, but their B cell receptore (BCR) sequence may differ due to the accumulation of somatic hypermutations (SHMs). Clonal relationships are learned from AIRR-seq data by analyzing the BCR sequence, with the most common methods focused on the highly diverse junction region. However, clonally related cells often share SHMs which have been accumulated during affinity maturation. Here, we investigate whether shared SHMs in the V and J segments of the BCR can be leveraged along with the junction sequence to improve the ability to identify clonally related sequences. We develop independent distance functions that capture junction similarity and shared mutations, and combine these in a spectral clustering framework to infer the BCR clonal relationships. Using both simulated and experimental data, we show that this model improves both the sensitivity and specificity for identifying B cell clones.AvailabilitySource code for this method is freely available in the SCOPer (Spectral Clustering for clOne Partitioning) R package (version 0.2 or later) in the Immcantation framework: www.immcantation.org under the CC BY-SA 4.0 [email protected]

scholarly journals GLaMST: grow lineages along minimum spanning tree for b cell receptor sequencing data

BMC Genomics ◽  
2020 ◽  
Vol 21 (S9) ◽  
Author(s):  
Xingyu Yang ◽  
Christopher M. Tipton ◽  
Matthew C. Woodruff ◽  
Enlu Zhou ◽  
F. Eun-Hyung Lee ◽  
...  
Keyword(s):  
B Cell ◽  
Spanning Tree ◽  
Minimum Spanning Tree ◽  
Somatic Hypermutation ◽  
Ground Truth ◽  
Affinity Maturation ◽  
Sequencing Analysis ◽  
Sequencing Data ◽  
Lineage Tree ◽  
Lineage Trees

Abstract Background B cell affinity maturation enables B cells to generate high-affinity antibodies. This process involves somatic hypermutation of B cell immunoglobulin receptor (BCR) genes and selection by their ability to bind antigens. Lineage trees are used to describe this microevolution of B cell immunoglobulin genes. In a lineage tree, each node is one BCR sequence that mutated from the germinal center and each directed edge represents a single base mutation, insertion or deletion. In BCR sequencing data, the observed data only contains a subset of BCR sequences in this microevolution process. Therefore, reconstructing the lineage tree from experimental data requires algorithms to build the tree based on partially observed tree nodes. Results We developed a new algorithm named Grow Lineages along Minimum Spanning Tree (GLaMST), which efficiently reconstruct the lineage tree given observed BCR sequences that correspond to a subset of the tree nodes. Through comparison using simulated and real data, GLaMST outperforms existing algorithms in simulations with high rates of mutation, insertion and deletion, and generates lineage trees with smaller size and closer to ground truth according to tree features that highly correlated with selection pressure. Conclusions GLaMST outperforms state-of-art in reconstruction of the BCR lineage tree in both efficiency and accuracy. Integrating it into existing BCR sequencing analysis frameworks can significant improve lineage tree reconstruction aspect of the analysis.

scholarly journals GLaMST: Grow Lineages along Minimum Spanning Tree for B Cell Receptor Sequencing Data

2018 ◽  
Author(s):  
Xingyu Yang ◽  
Christopher M. Tipton ◽  
Matthew C. Woodruff ◽  
Enlu Zhou ◽  
F. Eun-Hyung Lee ◽  
...  
Keyword(s):  
B Cell ◽  
Spanning Tree ◽  
Minimum Spanning Tree ◽  
Somatic Hypermutation ◽  
Ground Truth ◽  
Affinity Maturation ◽  
Sequencing Data ◽  
Single Base ◽  
Lineage Tree ◽  
Lineage Trees

AbstractB cell affinity maturation enables B cells to generate high-affinity antibodies. This process involves somatic hypermutation of B cell immunoglobulin receptor (BCR) genes and selection by their ability to bind antigens. Lineage trees are used to describe this microevolution of B cell immunoglobulin genes. In a lineage tree, each node is one BCR sequence that mutated from the germinal center and each directed edge represents a single base mutation, insertion or deletion. In BCR sequencing data, the observed data only contains a subset of BCR sequences in this microevolution process. Therefore, reconstructing the lineage tree from experimental data requires algorithms to build the tree based on partially observed tree nodes. We developed a new algorithm named Grow Lineages along Minimum Spanning Tree (GLaMST), which efficiently reconstruct the lineage tree given observed BCR sequences that correspond to a subset of the tree nodes. GLaMST constructs the minimum-spanning-tree (MST) to approximate the landscape of how observed BCR sequences are related, uses the MST to guide the interpolation of the closest unobserved sequence, updates the MST for the interpolation of additional unobserved sequences, and iterates until a full lineage tree is completed, where all observed sequences are connected by interpolated unobserved sequences and single base operations of mutations, insertions and deletions. Through comparison using simulated and real data, GLaMST outperforms existing algorithms in simulations with high rates of mutation, insertion and deletion, and generates lineage trees with smaller size and closer to ground truth according to tree features that highly correlated with selection pressure.

scholarly journals Mechanisms behind Functional Avidity Maturation in T Cells

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Marina Rode von Essen ◽  
Martin Kongsbak ◽  
Carsten Geisler
Keyword(s):  
T Cells ◽  
T Cell ◽  
B Cell ◽  
Somatic Hypermutation ◽  
Cell Receptor ◽  
Affinity Maturation ◽  
Functional Avidity ◽  
Cell Clones ◽  
Genes Encoding ◽  
Avidity Maturation

During an immune response antigen-primed B-cells increase their antigen responsiveness by affinity maturation mediated by somatic hypermutation of the genes encoding the antigen-specific B-cell receptor (BCR) and by selection of higher-affinity B cell clones. Unlike the BCR, the T-cell receptor (TCR) cannot undergo affinity maturation. Nevertheless, antigen-primed T cells significantly increase their antigen responsiveness compared to antigen-inexperienced (naïve) T cells in a process called functional avidity maturation. This paper covers studies that describe differences in T-cell antigen responsiveness during T-cell differentiation along with examples of the mechanisms behind functional avidity maturation in T cells.

EBV Transformation of Tonsil Germinal Centre B Cells Carrying Functionally Inactivated IgV Gene.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3248-3248
Author(s):  
Sridhar Chaganti ◽  
Noelia Begue Pastor ◽  
Mark T. Drayson ◽  
Andy I. Bell ◽  
Alan B. Rickinson
Keyword(s):  
B Cells ◽  
B Cell ◽  
Somatic Hypermutation ◽  
B Cell Lymphoma ◽  
Affinity Maturation ◽  
Germinal Centre ◽  
Chain Gene ◽  
Lymphoid Tissues ◽  
Memory B Cell

Abstract Somatic hypermutation of immunoglobulin (Ig) gene sequences in the germinal centres of lymphoid tissues is necessary for affinity maturation of B cell responses to antigen challenge. This process generates a few clones with improved affinity that are selected into B cell memory and many clones with other non favourable Ig mutations, including some cells with functionally inactivated Ig gene that normally die by apoptosis. It is postulated that infection with Epstein-Barr virus (EBV), a B lymphotropic agent linked to several types of B cell lymphoma, can rescue germinal centre cells with unfavourable mutations. This creates a pool of infected cells at greater risk of developing into lymphomas. In the present work, CD38+ germinal centre B cells were separated from tonsil by negative selection for IgD and CD39. Peripheral blood naïve and memory B cell subpopulations were FACS sorted as IgD+, CD27− and IgD−, CD27+ fractions respectively. These cells were infected with EBV (B95.8 strain) in vitro and seeded at limiting dilutions onto fibroblast feeders. EBV transformed lymphoblastoid cell lines (LCLs) from such cultures were analysed for surface Ig phenotype. Naïve B cell transformants were consistently IgM+, IgD+. Memory B cell transformants were IgM+ in some cases but more frequently IgG+ or IgA+. Germinal centre transformants showed the same spectrum of surface Ig phenotypes as memory cell transformants but in addition we identified six germinal centre derived LCLs which were consistently surface Ig negative. Sequencing from these lines confirmed that in at least three cases EBV had rescued cells with functionally inactivated Ig heavy chain gene.

scholarly journals Performance-optimized partitioning of clonotypes from high-throughput immunoglobulin repertoire sequencing data

2017 ◽  
Author(s):  
Nima Nouri ◽  
Steven H. Kleinstein
Keyword(s):  
Sensitivity And Specificity ◽  
High Throughput ◽  
Hamming Distance ◽  
Somatic Hypermutation ◽  
Simulated Data ◽  
Automate Method ◽  
Sequencing Data ◽  
Single Linkage ◽  
Adaptive Immune ◽  
Repertoire Sequencing

AbstractMotivationDuring adaptive immune responses, activated B cells expand and undergo somatic hypermutation of their immunoglobulin (Ig) receptor, forming a clone of diversified cells that can be related back to a common ancestor. Identification of B cell clonotypes from high-throughput Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) data relies on computational analysis. Recently, we proposed an automate method to partition sequences into clonal groups based on single-linkage clustering of the Ig receptor junction region with length-normalized hamming distance metric. This method could identify clonally-related sequences with high confidence on several benchmark experimental and simulated data sets. However, this approach was computationally expensive, and unable to provide estimates of accuracy for new data. Here, a new method is presented that address this computational bottleneck and also provides a study-specific estimation of performance, including sensitivity and specificity. The method uses a finite mixture modeling fitting procedure for learning the parameters of two univariate curves which fit the bimodal distributions of the distance vector between pairs of sequences. These distribution are used to estimate the performance of different threshold choices for partitioning sequences into clonotypes. These performance estimates are validated using simulated and experimental datasets. With this method, clonotypes can be identified from AIRR-seq data with sensitivity and specificity profiles that are user-defined based on the overall goals of the study.AvailabilitySource code is freely available at the Immcantation Portal: www.immcantation.com under the CC BY-SA 4.0 [email protected]

scholarly journals Differential Genome-Wide Mutational Patterns in Indolent B-Cell Lymphomas

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 4102-4102
Author(s):  
Julieta Haydee Sepulveda Yanez ◽  
Diego Alvarez ◽  
Jose Fernandez-Goycoolea ◽  
Cornelis A.M. van Bergen ◽  
Hendrik Veelken ◽  
...  
Keyword(s):  
B Cell ◽  
Cell Lymphoma ◽  
R Package ◽  
Cpg Methylation ◽  
Unknown Etiology ◽  
Sequencing Data ◽  
B Cell Lymphomas ◽  
B Cell Malignancies ◽  
Mutational Signatures ◽  
Mutational Landscape

Abstract Introduction: In recent years, strategies have been developed to identify specific mutation patterns within next-generation sequencing data. Distinct mutational patterns can be linked to underlying mutagenic processes in human cancer. One approach analyzes single base substitutions in the context of their neighboring bases as trinucleotides. The relative prevalence of all possible 96 altered trinucleotides defines distinctive mutational signatures. The activity of activation-induced cytidine deaminase (AID) initiates a specific mutational process in B cells. AID induces deamination of deoxycytidine into deoxyuridine. Subsequent mechanisms to repair the resulting mismatch lead to different genomic alterations that can be assigned to three mutational signatures: a canonical signature characterized by C>T/G transitions at WRCY motifs, a non-canonical signature defined by A>C transversions at WAN motifs, and a third AID signature characterized by C>T transitions at RCG motifs with preference for methylated CpG (W: A or T; R: purine; Y: pyrimidine, N: any nucleotide). The latter signature has specifically been designated as AID-mediated CpG-methylation-dependent mutagenesis. AID activity has been linked to the pathogenesis of several B-cell lymphomas, including follicular lymphoma (FL), chronic lymphocytic leukemia (CLL), and mantle cell lymphoma (MCL). Therefore, we searched for the contribution of different AID signatures in these B-cell malignancies. Methods: We analyzed the mutational landscape in whole exome (WES) and whole genome (WGS) sequencing data from 41 FL, 30 CLL, 2 MBL, and 43 MCL cases. Somatic variants were called by comparison of tumor and germline DNA with an in-house developed pipeline. Mutational signatures were defined according to the 96-base substitution model (Alexandrov et al. 2013) by an unsupervised machine learning with implementation of the SomaticSignatures R package (Gehring et al. 2015). In addition, MutationalPattern R package (Blokzijl et al. 2018) was executed for comparison to mutational signatures defined in COSMIC. Results: In unsupervised analyses of FL, CLL/MBL, and MCL cases, 77% of the mutation spectrum variance was attributable to four signatures (S1-4). In FL, the mutational landscape was dominated by S4 characterized by mutations in both canonical and non-canonical AID motifs (40%, 95% CI: 35-76%). The second most frequent signature (S2; 27%, 21-49%) was characterized by C>A transitions in the context of the non-canonical AID and the CpG hotspot motifs (RCG). The mutational landscape of CLL and MBL was strongly dominated by signature S3 (50%, 45-95%). S3 contains mutations in RCG motifs as well as mutations in non-canonical AID motifs (NTW), but with a lower contribution that in S4. In contrast, the mutational landscape of MCL was dominated by S1 (31%, 24-55%) characterized by C>T transitions in the RCG motif in addition to a striking prevalence of the TCT>TTT transition that is known to be associated with the activity of APOBEC enzymes. In comparison to the mutational signatures in COSMIC, the lymphomas analyzed here carry a strong similarity to the COSMIC signatures 1, 5, and 25. These signatures are observed across a wide spectrum of cancer types and are either of unknown etiology (S5 and S25) or associated with age (S1). Conclusions: The most common point mutations in CLL/MBL and FL are C>T transitions and indicate a strong influence of AID on their mutational landscape. In the indolent B-cell malignancies, all three known AID-related signatures, i.e. canonical, non-canonical, and CpG-methylation-dependent can be found. In contrast, the genomic landscape of MCL is dominated by variants in CpG-methylation-dependent mutagenesis sites and by an APOBEC-related motif. In addition to AID-related signatures, we also found consensus signatures described in COSMIC such as the age-related spontaneous deamination signature 1. Our work independently confirms the role of AID in B-cell lymphoma pathogenesis but points to disease-specific mechanisms that modulate AID in the respective lymphoma cell of origin. In addition, our data suggest that distinctive repair mechanisms operate in different entities. Disclosures No relevant conflicts of interest to declare.

scholarly journals WASp Is Crucial for the Unique Architecture of the Immunological Synapse in Germinal Center B-Cells

2021 ◽  
Vol 9 ◽  
Author(s):  
Yanan Li ◽  
Anshuman Bhanja ◽  
Arpita Upadhyaya ◽  
Xiaodong Zhao ◽  
Wenxia Song
Keyword(s):  
B Cells ◽  
B Cell ◽  
Lipid Bilayers ◽  
Germinal Center ◽  
Actin Polymerization ◽  
Immunological Synapse ◽  
Somatic Hypermutation ◽  
Affinity Maturation ◽  
Membrane Protrusions ◽  
Germinal Center B Cells

B-cells undergo somatic hypermutation and affinity maturation in germinal centers. Somatic hypermutated germinal center B-cells (GCBs) compete to engage with and capture antigens on follicular dendritic cells. Recent studies show that when encountering membrane antigens, GCBs generate actin-rich pod-like structures with B-cell receptor (BCR) microclusters to facilitate affinity discrimination. While deficiencies in actin regulators, including the Wiskott-Aldrich syndrome protein (WASp), cause B-cell affinity maturation defects, the mechanism by which actin regulates BCR signaling in GBCs is not fully understood. Using WASp knockout (WKO) mice that express Lifeact-GFP and live-cell total internal reflection fluorescence imaging, this study examined the role of WASp-mediated branched actin polymerization in the GCB immunological synapse. After rapid spreading on antigen-coated planar lipid bilayers, GCBs formed microclusters of phosphorylated BCRs and proximal signaling molecules at the center and the outer edge of the contact zone. The centralized signaling clusters localized at actin-rich GCB membrane protrusions. WKO reduced the centralized micro-signaling clusters by decreasing the number and stability of F-actin foci supporting GCB membrane protrusions. The actin structures that support the spreading membrane also appeared less frequently and regularly in WKO than in WT GCBs, which led to reductions in both the level and rate of GCB spreading and antigen gathering. Our results reveal essential roles for WASp in the generation and maintenance of unique structures for GCB immunological synapses.

scholarly journals Distinct clonal evolution of B-cells in HIV controllers with neutralizing antibody breadth

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Deniz Cizmeci ◽  
Giuseppe Lofano ◽  
Evan Rossignol ◽  
Anne-Sophie Dugast ◽  
Dongkyoon Kim ◽  
...  
Keyword(s):  
B Cells ◽  
B Cell ◽  
Somatic Hypermutation ◽  
Clonal Evolution ◽  
Neutralizing Antibody ◽  
Affinity Maturation ◽  
Gene Repertoire ◽  
Immunoglobulin Gene ◽  
Hiv Controllers ◽  
Hiv 1

A minor subset of individuals infected with HIV-1 develop antibody neutralization breadth during the natural course of the infection, often linked to chronic, high-level viremia. Despite significant efforts, vaccination strategies have been unable to induce similar neutralization breadth and the mechanisms underlying neutralizing antibody induction remain largely elusive. Broadly neutralizing antibody responses can also be found in individuals who control HIV to low and even undetectable plasma levels in the absence of antiretroviral therapy, suggesting that high antigen exposure is not a strict requirement for neutralization breadth. We therefore performed an analysis of paired heavy and light chain B-cell receptor (BCR) repertoires in 12,591 HIV-1 envelope-specific single memory B-cells to determine alterations in the BCR immunoglobulin gene repertoire and B-cell clonal expansions that associate with neutralizing antibody breadth in 22 HIV controllers. We found that the frequency of genomic mutations in IGHV and IGLV was directly correlated with serum neutralization breadth. The repertoire of the most mutated antibodies was dominated by a small number of large clones with evolutionary signatures suggesting that these clones had reached peak affinity maturation. These data demonstrate that even in the setting of low plasma HIV antigenemia, similar to what a vaccine can potentially achieve, BCR selection for extended somatic hypermutation and clonal evolution can occur in some individuals suggesting that host-specific factors might be involved that could be targeted with future vaccine strategies.

scholarly journals Multiscale affinity maturation simulations to elicit HIV broadly neutralizing antibodies

2021 ◽  
Author(s):  
Kayla Sprenger ◽  
Simone Conti ◽  
Victor Ovchinnikov ◽  
Arup K Chakraborty ◽  
martin karplus
Keyword(s):  
Neutralizing Antibodies ◽  
Adaptive Immune System ◽  
Multiscale Model ◽  
Cell Receptor ◽  
Affinity Maturation ◽  
Sequencing Data ◽  
Broadly Neutralizing Antibodies ◽  
Adaptive Immune ◽  
Cd4 Binding Site ◽  
Anti Hiv

The design of vaccines against highly mutable pathogens, such as HIV and influenza, requires a detailed understanding of how the adaptive immune system responds to encountering multiple variant antigens (Ags). Here, we describe a multiscale model of B cell receptor (BCR) affinity maturation that employs actual BCR nucleotide sequences and treats BCR/Ag interactions in atomistic detail. We apply the model to simulate the maturation of a broadly neutralizing Ab (bnAb) against HIV. Starting from a germline precursor sequence of the VRC01 anti-HIV Ab, we simulate BCR evolution in response to different vaccination protocols and different Ags, which were previously designed by us. The simulation results provide qualitative guidelines for future vaccine design and reveal unique insights into bnAb evolution against the CD4 binding site of HIV. Our model makes possible direct comparisons of simulated BCR populations with results of deep sequencing data, which will be explored in future applications.

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