A Public Database of Memory and Naive B-Cell Receptor Sequences

DeWitt, William S; Lindau, Paul; Snyder, Thomas M.; Sherwood, Anna; Vignali, Marissa; Carlson, Christopher S.; Greenberg, Philip D.; Duerkopp, Natalie; Emerson, Ryan; Robins, Harlan

doi:10.1371/journal.pone.0160853

Cited by 136 publications

(152 citation statements)

References 61 publications

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“…Public gut clonotypes appeared to undergo the strongest affinity maturation because CDR3 length for these clonotypes was significantly shorter ( P < 0.0001) than memory clonotypes whereas private gut–liver clonotypes were similar ( P > 0.05). Applying the same definitions for naive and memory, we compared SHM counts and confirmed they were significantly lower for naive than memory clonotypes (naive, 1.30 ± 0.6; memory, 6.13 ± 3.2; P < 0.0001), which again was consistent with reported results . SH3 counts for private gut–liver clonotypes, public gut clonotypes, and public liver clonotypes were all significantly higher than naive clonotypes ( P < 0.0001) but similar to one another (private gut–liver, 5.5 ± 3.2; public gut, 5.4 ± 3.4; public liver, 5.1 ± 2.7; P > 0.05) (Fig.…”

Section: Resultssupporting

confidence: 87%

“…The average CDR3 length for naive and memory clonotypes differed significantly (naive, 54.3 ± 11.8 nt; memory, 51.9 ± 10.8; P < 0.0001) (Fig. A), which is consistent with findings that affinity maturation results in shorter CDR3 lengths . We next compared the CDR3 lengths of overlapping private and public clonotypes and determined that private gut–liver clonotypes and public gut clonotypes appeared significantly different than naive (private gut–liver, 52.0 ± 10.3 nt; public gut, 42.0 ± 6.6 nt; naive, 54.3 ± 11.8 nt; P < 0.0001) (Fig.…”

Section: Resultssupporting

confidence: 83%

“…C). Both B‐cell repertories appeared substantially more clonal than sorted and sequenced CD19+CD27+ memory B cells from the peripheral blood of healthy controls . Together, these findings indicate that B cells in the gut undergo greater clonal expansion compared to the liver.…”

Section: Resultsmentioning

confidence: 81%

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Gut and Liver B Cells of Common Clonal Origin in Primary Sclerosing Cholangitis–Inflammatory Bowel Disease

Chung

Henriksen

Jørgensen

et al. 2018

Hepatology Communications

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B cells express an antigen‐specific B‐cell receptor (BCR) and may contribute to liver inflammation by recognizing shared antigens in the gut and liver. Herein, we used high‐throughput BCR sequencing of the immunoglobulin heavy chain, specifically the complementarity‐determining region 3 (CDR3), to characterize the B‐cell repertoire of freshly‐frozen paired gut and liver tissue samples from patients with primary sclerosing cholangitis (PSC) and concurrent inflammatory bowel disease (IBD) (PSC‐IBD, n = 10) and paired formalin‐fixed paraffin‐embedded (FFPE) tumor‐adjacent normal colon and liver tissue from patients with colorectal liver metastases (controls, n = 10). We observed significantly greater numbers of B cells (P < 0.01) and unique B‐cell clonotypes (P < 0.05) in gut samples compared to liver samples of patients with PSC‐IBD, whereas BCR sequences in FFPE normal gut and liver samples were nearly absent (14 ± 5 clonotypes; mean ± SD; n = 20). In PSC‐IBD, an average of 8.3% (range, 1.6%‐18.0%) of B‐cell clonotypes were found to overlap paired gut and liver samples following the exclusion of memory clonotypes reported in the blood of healthy controls. Overlapping gut and liver clonotypes showed stronger evidence of antigen‐driven activation compared to non‐overlapping clonotypes, including shorter CDR3 lengths and higher counts of somatic hypermutation (P < 0.0001). Conclusion: A proportion of gut and liver B cells originate from a common clonal origin (i.e., likely to recognize the same antigen) in patients with PSC which suggests B‐cell antigens are shared across the gut–liver axis. (Hepatology Communications 2018; 00:000‐000)

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Section: Resultssupporting

confidence: 87%

Section: Resultssupporting

confidence: 83%

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Gut and Liver B Cells of Common Clonal Origin in Primary Sclerosing Cholangitis–Inflammatory Bowel Disease

Chung

Henriksen

Jørgensen

et al. 2018

Hepatology Communications

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“…12,13 In brief, libraries of rearranged Ig loci were generated from tumor gDNA by multiplex polymerase chain reaction (PCR) using sense primers specific for all variable (V) (and diversity [D]) gene segments and antisense primers specific for all joining (J) gene segments for the IGH and IGK/ IGL loci. The inclusion of primers specific for IGHD enabled the capture of incomplete IGHD to IGHJ (DJ) rearrangements.…”

Section: Hts Of Igh and Igk/igl Chainsmentioning

confidence: 99%

High-throughput sequencing of the B-cell receptor in African Burkitt lymphoma reveals clues to pathogenesis

et al. 2017

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• High-throughput sequencing of primary African Burkitt lymphoma tumors suggests disrupted immunoglobulin rearrangements in BL progenitors.• Extensive mutation of expressed and nonexpressed IGH rearrangements suggests multiple active mutational processes in BL tumors. suggesting that the target of ongoing mutagenesis of these loci in BL tumor cells is not limited to expressed alleles. IGHV usage in both BL tumor cohorts revealed enrichment for IGHV genes that are infrequently used in memory B cells from healthy subjects. Analysis of publicly available DNA sequencing and RNAseq data revealed that these same IGHV genes were overrepresented in dominant tumor-associated IGH rearrangements in several independent BL tumor cohorts. These data suggest that BL derives from an abnormal B-cell progenitor and that aberrant mutational processes are active on the immunoglobulin loci in BL cells.

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“…For a given individual, the number of unique B cells is estimated to be greater than 10 7 (22), and analysis of antigen-specific B cells may require sequencing of up to 10 4 or 10 5 unique B cells (23). The Illumina deep-sequencing technology is capable of providing sufficient sequencing depth to capture this repertoire in its entirety for sequence read lengths of ~150 bp (24).…”

Section: Introductionmentioning

confidence: 99%

BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires

et al. 2017

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The somatic diversity of antigen-recognizing B-cell receptors (BCRs) arises from Variable (V), Diversity (D), and Joining (J) (VDJ) recombination and somatic hypermutation (SHM) during B-cell development and affinity maturation. The VDJ junction of the BCR heavy chain forms the highly variable complementarity determining region 3 (CDR3), which plays a critical role in antigen specificity and binding affinity. Tracking the selection and mutation of the CDR3 can be useful in characterizing humoral responses to infection and vaccination. Although tens to hundreds of thousands of unique BCR genes within an expressed B-cell repertoire can now be resolved with high-throughput sequencing, tracking SHMs is still challenging because existing annotation methods are often limited by poor annotation coverage, inconsistent SHM identification across the VDJ junction, or lack of B-cell lineage data. Here, we present B-cell repertoire inductive lineage and immunosequence annotator (BRILIA), an algorithm that leverages repertoire-wide sequencing data to globally improve the VDJ annotation coverage, lineage tree assembly, and SHM identification. On benchmark tests against simulated human and mouse BCR repertoires, BRILIA correctly annotated germline and clonally expanded sequences with 94 and 70% accuracy, respectively, and it has a 90% SHM-positive prediction rate in the CDR3 of heavily mutated sequences; these are substantial improvements over existing methods. We used BRILIA to process BCR sequences obtained from splenic germinal center B cells extracted from C57BL/6 mice. BRILIA returned robust B-cell lineage trees and yielded SHM patterns that are consistent across the VDJ junction and agree with known biological mechanisms of SHM. By contrast, existing BCR annotation tools, which do not account for repertoire-wide clonal relationships, systematically underestimated both the size of clonally related B-cell clusters and yielded inconsistent SHM frequencies. We demonstrate BRILIA’s utility in B-cell repertoire studies related to VDJ gene usage, mechanisms for adenosine mutations, and SHM hot spot motifs. Furthermore, we show that the complete gene usage annotation and SHM identification across the entire CDR3 are essential for studying the B-cell affinity maturation process through immunosequencing methods.

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A Public Database of Memory and Naive B-Cell Receptor Sequences

Cited by 136 publications

References 61 publications

Gut and Liver B Cells of Common Clonal Origin in Primary Sclerosing Cholangitis–Inflammatory Bowel Disease

Gut and Liver B Cells of Common Clonal Origin in Primary Sclerosing Cholangitis–Inflammatory Bowel Disease

High-throughput sequencing of the B-cell receptor in African Burkitt lymphoma reveals clues to pathogenesis

BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires

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