A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data

Nouri, Nima; Kleinstein, Steven H.

doi:10.1093/bioinformatics/bty235

Cited by 74 publications

(103 citation statements)

References 30 publications

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“…Caveats should be noted given that our results rely on tracing B cell clones by analysis of their IGH V(D)J sequences alone. While we (and others) have demonstrated that clonal relationships can be reliably inferred given the diversity of IGH V(D)J sequences, false positives may occur (43,67,68). Additionally, owing to the abundance of transitional B cells that re-populate the repertoire during RTX relapse and our interest in studying antigen-experienced B cell subsets, we specifically excluded IgD+ expressing B cell subsets from our single-cell analysis.…”

Section: Discussionmentioning

confidence: 99%

Single-cell repertoire tracing identifies rituximab refractory B cells during myasthenia gravis relapses

Jiang

Fichtner

Hoehn

et al. 2019

Preprint

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One Sentence Summary: Disease relevant B cells during post-rituximab (RTX) relapse emerge from the unsuccessful depletion of pre-existing B cell clones; single-cell transcriptomic phenotyping combined with lineage tracing using paired B cell receptor repertoires identified both persistent antibody-secreting cell as well as memory B cell subsets.Abstract: Rituximab, an anti-CD20 B cell-depleting therapy, is indicated to treat a growing number of autoimmune disorders. However, disease relapses can occur when the B cell compartment is re-established after treatment. To explore the mechanism of relapse, we studied patients with muscle-specific kinase (MuSK) myasthenia gravis (MG), a paradigm for B cellmediated autoimmune diseases in which pathology is directly associated with autoantibody production. Whether the failed depletion of specific clones leads to the persistence of autoantibody producing B cell subsets has yet to be elucidated. Here we show that rituximab (RTX) therapy is not fully effective at eliminating disease-associated B cells and provide a mechanistic understanding of relapse. We carried out single-cell transcriptional and B cell receptor (BCR) profiling on longitudinal B cell samples from the peripheral blood of MuSK MG patients who relapsed after rituximab therapy. Computational analysis of these data identified individual B cells that were refractory to rituximab depletion by linking them to clones that were present prior to therapy and continued to persist after therapy. These persistent B cell clones were present at high frequency, and included both antibody-secreting cells and memory B cells. They were disproportionately isotype switched with elevated somatic hypermutation frequencies and a gene expression signature associated with antigen-experience and B cell clonal expansion. We further identified both antibody-secreting cells and memory B cells with specificity for MuSK autoantigen that were clonally expanded during relapse and persistent. Our results provide evidence that post-rituximab relapse in MuSK MG is associated with the failed depletion of autoantigen-specific B cell subsets. This work provides insight into the durability of human B cells during treatment with therapeutic CD20-specific monoclonal antibodies. The transcriptional signatures associated with B cell resistance may represent new therapeutic avenues for treatment and biomarkers of depletion efficacy.

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Section: Discussionmentioning

confidence: 99%

Single-cell repertoire tracing identifies rituximab refractory B cells during myasthenia gravis relapses

Jiang

Fichtner

Hoehn

et al. 2019

Preprint

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“…The original distance-based model for identification of B cell clones used by SCOPer measures distance using the junction region of the BCR (Nouri and Kleinstein, 2018b). The junction includes the CDR3 along with the two flanking amino acids (one 5 that is encoded by IGHV, and one 3 that is encoded by IGHJ) (Lefranc, 2014).…”

Section: The Stress-based Methods Improves the Sensitivity Specificitmentioning

confidence: 99%

“…This model is implemented in the new version of SCOPer. The first version of SCOPer, a spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data, was presented in Nouri and Kleinstein (2018b). In the following sections, we discuss the main steps of the methodology and explain our implementation of the recent improvements upon the original framework.…”

Section: Figmentioning

confidence: 99%

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

Nouri

Kleinstein

2019

Preprint

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Motivation: Adaptive 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 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 CDR3 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 CDR3 sequence to improve the ability to identify clonally related sequences. We develop independent distance functions that capture shared mutations and CDR3 similarity, and combine these in a spectral clustering framework. Using simulated data, we show that this model improves both the sensitivity and specificity for identifying clonal relationships. Availability: Source code for this method is freely available in the SCOPer (Spectral Clustering for clOne Partitioning) R package (version 0.2 or newer) in the Immcantation framework: www.immcantation.org under the CC BY-SA 4.0 license.

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“…A hamming distance is calculated on the junction regions of pairs of sequences in each of the groups separately. Finally, distances are fed into a clustering algorithm (Hierarchical [1] or Spectral [2]). Here, we propose to use a tf-idf based distance that bypasses the three steps prior to clustering, and is not restricted to sequences with the same V or J gene or junction length.…”

Section: Introductionmentioning

confidence: 99%

Alignment free identification of clones in B cell receptor repertoires

Lindenbaum

Nouri

Kluger

et al. 2020

Preprint

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Following pathogenic challenge, activated B cells rapidly expand and undergo somatic hypermutation, yielding groups of clonally related B-cells with diversified immunoglobulin receptors. Inference of clonal relationships based on the receptor sequence is an essential step in many adaptive immune receptor repertoire sequencing studies. These relationships are typically identified by a multi-step process that involves: (1) grouping sequences based on shared V and J gene assignments, and junction lengths, and (2) clustering these sequences using a junction-based distance. However, this approach is sensitive to the initial V(D)J gene assignments, which are error-prone, and fails to identify clonal relatives whose junction length has changed through accumulation of indels. Through defining a translation-invariant feature space in which we cluster the sequences, we develop an alignment-free clonal identification method that does not require gene assignments and is not restricted to a fixed junction length. This alignment-free approach has higher sensitivity compared to a typical junction-based distance method without loss of specificity and PPV. While the alignment-free procedure identifies clones that are broadly consistent with the junction-based distance method, it also identifies clones with characteristics (multiple V or J gene assignments or junction lengths) that are not detectable with the junction based distance method.

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A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data

Cited by 74 publications

References 30 publications

Single-cell repertoire tracing identifies rituximab refractory B cells during myasthenia gravis relapses

Single-cell repertoire tracing identifies rituximab refractory B cells during myasthenia gravis relapses

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

Alignment free identification of clones in B cell receptor repertoires

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