scholarly journals 67 B-cell receptor heavy chain repertoire profiling using an augmented transcriptome

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A72-A72
Author(s):  
Eric Levy ◽  
Pamela Milani ◽  
Gabor Bartha ◽  
Charles Abbott ◽  
Robert Power ◽  
...  
Keyword(s):  
B Cell ◽  
Heavy Chain ◽  
Solid Tumor ◽  
Clonal Diversity ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Ffpe Sample ◽  
Response To Treatment ◽  
Ffpe Tumor ◽  
Ffpe Samples

BackgroundComprehensive profiling of the tumor and tumor microenvironment (TME) is a critical tool for furthering our understanding of tumor progression and response to treatment, including immunotherapies. To address this challenge, we developed an augmented, immuno-oncology-optimized exome/transcriptome platform, ImmunoID NeXTTM, which provides a more comprehensive view of the tumor and TME from limited FFPE tumor biopsies. We have recently added the ability to profile the B-cell receptor (BCR) heavy chain. Here, we show that ImmunoID NeXT is now able to accurately and reproducibly profile abundant B-cell clones and provide information on the diversity of B-cells in tumor samples.MethodsWe analyzed multiple replicates of PBMCs to examine the reproducibility of BCR sequence identification using ImmunoID NeXT. Utilizing a standalone BCR sequencing approach, we further evaluated the concordance of top clones to those identified by ImmunoID NeXT. In addition, we analyzed the reproducibility of BCR sequences in patient-derived FFPE samples. Finally, we used ImmunoID NeXT to profile the B-cell clonal diversity across over 500 solid tumor samples.ResultsReproducibility in PBMC samples was very high, with abundances of clones shared between replicates being very concordant (R2>0.92, R2>0.86, and R2>0.97 for IgG, IgM, and IgA, respectively). When comparing to a standalone BCR sequencing method that profiles IgM and IgG, we observed highly concordant abundances (R2>0.72 and R2>0.82 in IgM and IgG, respectively), as well as strong overlaps of top clones. When comparing subsequent curls of a tumor FFPE sample, we also achieved a high concordance of clonal abundances (R2>0.92, R2>0.93, and R2>0.76 for IgG, IgM, and IgA, respectively). Finally, we observed differences in clonal diversity of B-cell repertoires across over 500 solid tumor samples.ConclusionsWe demonstrate that ImmunoID NeXT can be used to reproducibly, sensitively, and accurately profile high-abundance BCR heavy chain clones, including coverage of all major isotypes. In addition, we show how ImmunoID NeXT can profile the diversity of the BCR repertoire across a variety of tumor samples. Combined with the platform’s TCR profiling capabilities, ImmunoID NeXT can provide insight into the diversity of the immune repertoire, contributing to its ability to provide comprehensive analysis of both the tumor and TME from a single FFPE sample.

scholarly journals Characterization of B-cell Receptor Heavy Chain Complementarity-determining Region 3 Repertoire Based on the Differences of Symbiotic Microorganisms in the Gut of Mice

2021 ◽  
Author(s):  
Jun Li ◽  
Yurong Pan ◽  
Qingqing Ma ◽  
Long Ma ◽  
Bin Shi ◽  
...  
Keyword(s):  
Small Intestine ◽  
B Cells ◽  
B Cell ◽  
Heavy Chain ◽  
Intestinal Microflora ◽  
Cell Receptor ◽  
Memory B Cells ◽  
B Cell Receptor ◽  
Positive Effects ◽  
Significant Difference

Abstract Background Colonization of gut microorganism is related to maturation of B cells in peripheral immune organs. This study aims to investigate the effect of intestinal microflora in Germ-free (GF), Specific Pathogen-free (SPF) and Clean (CL) BALB/C mice to small intestine total B-cell and memory B-cell receptor (BCR) complementary-determining region 3 (CDR3) repertoire. Results The composition and characteristics of intestinal microflora were analyzed by 16S rDNA sequencing. Genomic DNA extracted from small intestine tissue and memory B-cells of GF, SPF and CL mice were conducted via high-throughput DNA sequencing methods. As expected, significant differences of gut microflora diversity were observed in the three mice groups. CL group showed the most diversity, followed by SPF group, and GF group had the lowest diversity. Moreover, anormogenesis of intestinal lymphoid tissue were observed in GF mice. Diversity of the BCR heavy chain CDR3 repertoire in memory B cells were significant difference among three groups, but not in total B cells. The nucleotide polymorphism, usage frequency of gene segments (V, D, J, V–J gene segments) and amino acid of total B cells and memory B cells CDR3 were comparable among three mice groups, and there was significant difference between CL and GF mice groups. Conclusions The results of this study advocate that the colonization of intestinal microorganisms affect the diversity of B cells CDR3 repertoire. Elucidating mechanism of microbiome participated in the function of intestinal mucosal immune system may have positive effects on human health, and it requires further investigation.

scholarly journals Immunoglobulin heavy chains are sufficient to determine most B cell clonal relationships1

2019 ◽  
Author(s):  
Julian Q. Zhou ◽  
Steven H. Kleinstein
Keyword(s):  
B Cell ◽  
High Throughput ◽  
Heavy Chain ◽  
Clonal Expansion ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Light Chains ◽  
Heavy Chains ◽  
Computational Inference ◽  
Cell Clonal Expansion

AbstractB cell clonal expansion is vital for adaptive immunity. High-throughput B cell receptor (BCR) sequencing enables investigating this process, but requires computational inference to identify clonal relationships. This inference usually relies on only the BCR heavy chain, as most current protocols do not preserve heavy:light chain pairing. The extent to which paired light chains aids inference is unknown. Using human single-cell paired BCR datasets, we assessed the ability of heavy chain-based clonal clustering to identify clones. Of the expanded clones identified, <20% grouped cells expressing inconsistent light chains. Heavy chains from these misclustered clones contained more distant junction sequences and shared fewer V segment mutations than the accurate clones. This suggests that additional heavy chain information could be leveraged to refine clonal relationships. Conversely, light chains were insufficient to refine heavy chain-based clonal clusters. Overall, the BCR heavy chain alone is sufficient to identify clonal relationships with confidence.

The pre-B cell receptor and its role in proliferation and Ig heavy chain allelic exclusion

2002 ◽  
Vol 14 (5) ◽  
pp. 335-342 ◽  
Author(s):  
Inga-Lill Mårtensson ◽  
Antonius Rolink ◽  
Fritz Melchers ◽  
Cornelia Mundt ◽  
Steve Licence ◽  
...  
Keyword(s):  
B Cell ◽  
Heavy Chain ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Allelic Exclusion ◽  
Ig Heavy Chain

scholarly journals Variable heavy-chain gene analysis of follicular lymphomas: subclone selection rather than clonal evolution over time

Blood ◽  
2001 ◽  
Vol 98 (1) ◽  
pp. 238-240 ◽  
Author(s):  
Wilhelmina M. Aarts ◽  
Richard J. Bende ◽  
Janneke G. Bossenbroek ◽  
Steven T. Pals ◽  
Carel J. M. van Noesel
Keyword(s):  
B Cell ◽  
Heavy Chain ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Chain Gene ◽  
Variable Heavy ◽  
Vh Gene ◽  
Follicular Lymphomas ◽  
Receptor Evolution ◽  
Over Time

Abstract To investigate B-cell receptor evolution in follicular lymphomas (FLs), immunoglobulin variable heavy chain (VH) gene regions of 3 FLs were analyzed at different time points. One FL with a high somatic mutation load and intraclonal VH gene diversity was investigated in situ. VH gene transcripts were amplified and sequenced from samples of approximately 50 tumor cells isolated from frozen tissue sections by laser microdissection. Interestingly, the mutation pattern of the prevalent subclone in the relapse biopsy was virtually identical to that of a subclone isolated by microdissection from the presentation biopsy 9 years earlier. In a second FL, proof was obtained that the subclone that dominated the relapse sample had already been present in the initial biopsy. The finding that subclones found in the relapses of these FLs had not evolved over time but were preexistent, challenges the concept of antigen-driven B-cell receptor evolution during disease course.

scholarly journals Clonal Diversity of the B cell Receptor Repertoire in Patients with Coronary in-Stent Restenosis and Diabetes Mellitus

2020 ◽  
Author(s):  
Ruiqiang Weng ◽  
Sudong Liu ◽  
Xiaodong Gu ◽  
Zhixiong Zhong
Keyword(s):  
Diabetes Mellitus ◽  
B Cells ◽  
B Cell ◽  
Clonal Diversity ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Amino Acid Sequences ◽  
Common Amino Acid ◽  
Stent Restenosis ◽  
In Stent Restenosis

Abstract Background Coronary artery disease patients with diabetes mellitus may have a higher risk for clinical and angiographic restenosis. Evidence has suggested that B cells play a functional role in the progression of atherosclerotic lesions. The purpose of this study was to investigate the clonal diversity of the B cell receptor (BCR) repertoire in patients with coronary in-stent restenosis (ISR) and diabetes mellitus.Methods In the present study, we had enrolled 21 patients with ISR and DM or not and collected the peripheral blood mononuclear cell. The DNA was extrated and then we performed DNA-seq analysis to character the B-cell receptor profiles (BCR) of CAD patients with or without ISR. The BCR diversity and the overlap was evaluate by the bioinformatics base on the DNA-seq data.Result Seq-data showed that the diversity of amino acids was altered in patients with ISR. Specifically, 6 V gene segments as well as 41 V/J pairs exhibited different frequencies in patients with ISR, with the altered common amino acid sequences reaching 0.1–1.01% in ISR patients.Conclusion The present findings suggest that B cells may play a role in the occurrence of ISR and that further analysis of BCR profiles would enhance understanding of ISR.

scholarly journals Sequential activation and distinct functions for distal and proximal modules within the IgH 3′ regulatory region

2016 ◽  
Vol 113 (6) ◽  
pp. 1618-1623 ◽  
Author(s):  
Armand Garot ◽  
Marie Marquet ◽  
Alexis Saintamand ◽  
Sébastien Bender ◽  
Sandrine Le Noir ◽  
...  
Keyword(s):  
B Cells ◽  
B Cell ◽  
Heavy Chain ◽  
Somatic Hypermutation ◽  
Regulatory Region ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Receptor Expression ◽  
Class Switch ◽  
Cell Ontogeny

As a master regulator of functional Ig heavy chain (IgH) expression, the IgH 3′ regulatory region (3′RR) controls multiple transcription events at various stages of B-cell ontogeny, from newly formed B cells until the ultimate plasma cell stage. The IgH 3′RR plays a pivotal role in early B-cell receptor expression, germ-line transcription preceding class switch recombination, interactions between targeted switch (S) regions, variable region transcription before somatic hypermutation, and antibody heavy chain production, but the functional ranking of its different elements is still inaccurate, especially that of its evolutionarily conserved quasi-palindromic structure. By comparing relevant previous knockout (KO) mouse models (3′RR KO and hs3b-4 KO) to a novel mutant devoid of the 3′RR quasi-palindromic region (3′PAL KO), we pinpointed common features and differences that specify two distinct regulatory entities acting sequentially during B-cell ontogeny. Independently of exogenous antigens, the 3′RR distal part, including hs4, fine-tuned B-cell receptor expression in newly formed and naïve B-cell subsets. At mature stages, the 3′RR portion including the quasi-palindrome dictated antigen-dependent locus remodeling (global somatic hypermutation and class switch recombination to major isotypes) in activated B cells and antibody production in plasma cells.

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