The prospects of single‐cell analysis in autoimmunity

Sulen, André; Islam, Shahinul; Wolff, Anette S. B.; Oftedal, Bergithe E.

doi:10.1111/sji.12964

Cited by 4 publications

(3 citation statements)

References 160 publications

(276 reference statements)

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“…Goldstein and co-workers showed that single B cell sequencing can recover a higher number of antibody lineages compared to hybridoma technology ( Goldstein et al, 2019 ). Single-cell sequencing has also been used to identify SARS-CoV-2 specific Abs ( Woodruff et al, 2020 ; He et al, 2021 ), tumor-specific Abs ( Buus et al, 2021 ), and autoimmune disease-specific Abs ( Sulen et al, 2020 ; Jin et al, 2021 ). Single-cell sequencing is now readily available from several companies, including 10x Genomics and Takara Bio.…”

Section: B Cell Receptor Sequencingmentioning

confidence: 99%

Advances in antibody discovery from human BCR repertoires

Ismanto

Zhou

et al. 2022

Front. Bioinform.

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Antibodies make up an important and growing class of compounds used for the diagnosis or treatment of disease. While traditional antibody discovery utilized immunization of animals to generate lead compounds, technological innovations have made it possible to search for antibodies targeting a given antigen within the repertoires of B cells in humans. Here we group these innovations into four broad categories: cell sorting allows the collection of cells enriched in specificity to one or more antigens; BCR sequencing can be performed on bulk mRNA, genomic DNA or on paired (heavy-light) mRNA; BCR repertoire analysis generally involves clustering BCRs into specificity groups or more in-depth modeling of antibody-antigen interactions, such as antibody-specific epitope predictions; validation of antibody-antigen interactions requires expression of antibodies, followed by antigen binding assays or epitope mapping. Together with innovations in Deep learning these technologies will contribute to the future discovery of diagnostic and therapeutic antibodies directly from humans.

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Section: B Cell Receptor Sequencingmentioning

confidence: 99%

Advances in antibody discovery from human BCR repertoires

Ismanto

Zhou

et al. 2022

Front. Bioinform.

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“…Single-cell measurements have revolutionized our ability to study the variation within and between heterogeneous cell populations 1,2 . As single-cell RNA-sequencing (scRNA-seq) and other high-dimensional single-cell techniques have become increasingly accessible, these technologies have extended to studies including multiple experimental conditions, samples, or subjects.…”

Section: Introductionmentioning

confidence: 99%

Integrative, high-resolution analysis of single cells across experimental conditions with PARAFAC2

Ramirez,

Orcutt-Jahns,

Pascoe

et al. 2024

Preprint

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Effective tools for exploration and analysis are needed to extract insights from large-scale single-cell measurement data. However, current techniques for handling single-cell studies performed across experimental conditions (e.g., samples, perturbations, or patients) require restrictive assumptions, lack flexibility, or do not adequately deconvolute condition-to-condition variation from cell-to-cell variation. Here, we report that the tensor decomposition method PARAFAC2 (Pf2) enables the dimensionality reduction of single-cell data across conditions. We demonstrate these benefits across two distinct contexts of single-cell RNA-sequencing (scRNA-seq) experiments of peripheral immune cells: pharmacologic drug perturbations and systemic lupus erythematosus (SLE) patient samples. By isolating relevant gene modules across cells and conditions, Pf2 enables straightforward associations of gene variation patterns across specific patients or perturbations while connecting each coordinated change to certain cells without pre-defining cell types. The theoretical grounding of Pf2 suggests a unified framework for many modeling tasks associated with single-cell data. Thus, Pf2 provides an intuitive universal dimensionality reduction approach for multi-sample single-cell studies across diverse biological contexts.

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“…Secondary lymphoid organs, such as spleen and lymph nodes, have also been in focus in animal studies. The knowledge that the immune system also included other sites in the body came much later, but now when techniques are available that make it possible to isolate and study small populations of the cells, such as single cell RNA sequencing, 6 the field of tissue immunology has taken off.…”

mentioning

confidence: 99%