scholarly journals Single-cell sequencing reveals clonally expanded plasma cells during chronic viral infection produce virus-specific and cross-reactive antibodies

2021 ◽  
Author(s):  
Daniel Neumeier ◽  
Alessandro Pedrioli ◽  
Alessandro Genovese ◽  
Ioana Sandu ◽  
Roy Ehling ◽  
...  
Keyword(s):  
Viral Infection ◽  
Single Cell ◽  
Plasma Cell ◽  
Plasma Cells ◽  
Clonal Expansion ◽  
Chronic Viral Infection ◽  
Antibody Repertoire ◽  
Single Cell Sequencing ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractPlasma cells and their secreted antibodies play a central role in the long-term protection against chronic viral infection. However, due to experimental limitations, a comprehensive description of linked genotypic, phenotypic, and antibody repertoire features of plasma cells (gene expression, clonal frequency, virus specificity, and affinity) has been challenging to obtain. To address this, we performed single-cell transcriptome and antibody repertoire sequencing of the murine bone marrow plasma cell population following chronic lymphocytic choriomeningitis virus infection. Our single-cell sequencing approach recovered full-length and paired heavy and light chain sequence information for thousands of plasma cells and enabled us to perform recombinant antibody expression and specificity screening. Antibody repertoire analysis revealed that, relative to protein immunization, chronic infection led to increased levels of clonal expansion, class-switching, and somatic variants. Furthermore, antibodies from the highly expanded and class-switched (IgG) plasma cells were found to be specific for multiple viral antigens and a subset of clones exhibited cross-reactivity to non-viral- and auto-antigens. Integrating single-cell transcriptome data with antibody specificity suggested that plasma cell transcriptional phenotype was correlated to viral antigen specificity. Our findings demonstrate that chronic viral infection can induce and sustain plasma cell clonal expansion, combined with significant somatic hypermutation, and can generate cross-reactive antibodies. Graphical abstract.Single-cell sequencing reveals clonally expanded plasma cells during chronic viral infection produce virus-specific and cross-reactive antibodies.

scholarly journals singleCellHaystack: Finding surprising genes in 2-dimensional representations of single cell transcriptome data

2019 ◽  
Author(s):  
Alexis Vandenbon ◽  
Diego Diez
Keyword(s):  
Single Cell ◽  
Expression Patterns ◽  
R Package ◽  
Biological Knowledge ◽  
Transcriptome Data ◽  
Sequencing Data ◽  
Single Cell Sequencing ◽  
Leibler Divergence ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractSummarySingle-cell sequencing data is often visualized in 2-dimensional plots, including t-SNE plots. However, it is not straightforward to extract biological knowledge, such as differentially expressed genes, from these plots. Here we introduce singleCellHaystack, a methodology that addresses this problem. singleCellHaystack uses Kullback-Leibler Divergence to find genes that are expressed in subsets of cells that are non-randomly positioned on a 2D plot. We illustrate the usage of singleCellHaystack through applications on several single-cell datasets. singleCellHaystack is implemented as an R package, and includes additional functions for clustering and visualization of genes with interesting expression patterns.Availability and implementationhttps://github.com/alexisvdb/[email protected]

scholarly journals Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility

2019 ◽  
Author(s):  
Qiao Rui Xing ◽  
Chadi EL Farran ◽  
Yao Yi ◽  
Tushar Warrier ◽  
Pradeep Gautam ◽  
...  
Keyword(s):  
Single Cell ◽  
Target Genes ◽  
Chromatin Accessibility ◽  
Human Cell Lines ◽  
Microfluidic Chips ◽  
Primary Cells ◽  
Parallel Sequencing ◽  
Single Cell Sequencing ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

SUMMARYWe developed ASTAR-Seq (Assay for Single-cell Transcriptome and Accessibility Regions) integrated with automated microfluidic chips, which allows for parallel sequencing of transcriptome and chromatin accessibility within the same single-cell. Using ASTAR-Seq, we profiled 192 mESCs cultured in serum+LIF and 2i medium, 424 human cell lines including BJ, K562, JK1, and Jurkat, and 480 primary cells undergoing erythroblast differentiation. Integrative analysis using Coupled NMF identified the distinct sub-populations and uncovered sets of regulatory regions and the respective target genes determining their distinctions. Analysis of epigenetic regulomes further unravelled the key transcription factors responsible for the heterogeneity observed.

scholarly journals Single-cell sequencing of plasma cells from COVID-19 patients reveals highly expanded clonal lineages produce specific and neutralizing antibodies to SARS-CoV-2

2021 ◽  
Author(s):  
Roy A. Ehling ◽  
Cédric R. Weber ◽  
Derek M. Mason ◽  
Simon Friedensohn ◽  
Bastian Wagner ◽  
...  
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Plasma Cells ◽  
Critical Role ◽  
Antibody Repertoire ◽  
Single Cell Sequencing ◽  
Isolation And Characterization ◽  
Cell Antibody ◽  
Repertoire Sequencing ◽  
Potent Neutralization

ABSTRACTIsolation and characterization of antibodies in COVID-19 patients has largely focused on memory B cells, however it is the antibody-secreting plasma cells that are directly responsible for the production of serum antibodies, which play a critical role in controlling and resolving SARS-CoV-2 infection. To date there is little known about the specificity of plasma cells in COVID-19 patients. This is largely because plasma cells lack surface antibody expression, which complicates their screening. Here, we describe a technology pipeline that integrates single-cell antibody repertoire sequencing and high-throughput mammalian display screening to interrogate the specificity of plasma cells from 16 convalescent COVID-19 patients. Single-cell sequencing allows us to profile antibody repertoire features in these patients and identify highly expanded clonal lineages. Mammalian display screening is employed to reveal that 37 antibodies (out of 132 candidates) derived from expanded plasma cell clonal lineages are specific for SARS-CoV-2 antigens, including antibodies that target the receptor binding domain (RBD) with high affinity and exhibit potent neutralization of SARS-CoV-2.One Sentence SummarySingle-cell antibody repertoire sequencing and high-throughput screening identifies highly expanded plasma cells from convalescent COVID-19 patients that produce SARS-CoV-2-specific antibodies capable of potent neutralization.

scholarly journals Progress in Single Cell Sequencing Technology

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Qi Cai Ma ◽  
Wen Li Wu ◽  
Na Ye ◽  
Xin Dong Wang ◽  
Ping Yan ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Basic Unit ◽  
Sequencing Technology ◽  
Single Cell Sequencing ◽  
Physiological Diversity ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Whole Transcriptome ◽  
Life Structure

Cells are the basic unit of life structure and life activities. Because of the complex micro-environment of cells, the content of components that play a key role is relatively small, so single-cell analysis is extremely challenging. In recent years, single-cell sequencing technology has been developed and matured. Single-cell sequencing can reveal the composition and physiological diversity of cells, and the existing single-cell separation technology, single-cell whole genome amplification technology, single The principles and applications of cell whole transcriptome amplification technology and single cell transcriptome sequencing are summarized and summarized.

scholarly journals Barcode identification for single cell genomics

2017 ◽  
Author(s):  
Akshay Tambe ◽  
Lior Pachter
Keyword(s):  
Single Cell ◽  
Dna Barcode ◽  
De Bruijn Graph ◽  
Rna Seq ◽  
Single Cell Genomics ◽  
Single Cell Sequencing ◽  
Processing Step ◽  
De Bruijn ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractSingle-cell sequencing experiments use short DNA barcode ‘tags’ to identify reads that originate from the same cell. In order to recover single-cell information from such experiments, reads must be grouped based on their barcode tag, a crucial processing step that precedes other computations. However, this step can be difficult due to high rates of mismatch and deletion errors that can afflict barcodes. Here we present an approach to identify and error-correct barcodes by traversing the de Bruijn graph of circularized barcode k-mers. This allows for assignment of reads to consensus fingerprints constructed from k-mers, and we show that for single-cell RNA-Seq this improves the recovery of accurate single-cell transcriptome estimates.

scholarly journals Single cell transcriptome atlas of mouse mammary epithelial cells across development

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Bhupinder Pal ◽  
Yunshun Chen ◽  
Michael J. G. Milevskiy ◽  
François Vaillant ◽  
Lexie Prokopuk ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Single Cell ◽  
Developmental Stages ◽  
Mammary Epithelial Cells ◽  
Expression Profiles ◽  
Single Cells ◽  
Chromatin Accessibility ◽  
Mammary Epithelial ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Abstract Background Heterogeneity within the mouse mammary epithelium and potential lineage relationships have been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary ontogeny, we profiled single cells from nine different developmental stages spanning late embryogenesis, early postnatal, prepuberty, adult, mid-pregnancy, late-pregnancy, and post-involution, as well as the transcriptomes of micro-dissected terminal end buds (TEBs) and subtending ducts during puberty. Methods The single cell transcriptomes of 132,599 mammary epithelial cells from 9 different developmental stages were determined on the 10x Genomics Chromium platform, and integrative analyses were performed to compare specific time points. Results The mammary rudiment at E18.5 closely aligned with the basal lineage, while prepubertal epithelial cells exhibited lineage segregation but to a less differentiated state than their adult counterparts. Comparison of micro-dissected TEBs versus ducts showed that luminal cells within TEBs harbored intermediate expression profiles. Ductal basal cells exhibited increased chromatin accessibility of luminal genes compared to their TEB counterparts suggesting that lineage-specific chromatin is established within the subtending ducts during puberty. An integrative analysis of five stages spanning the pregnancy cycle revealed distinct stage-specific profiles and the presence of cycling basal, mixed-lineage, and 'late' alveolar intermediates in pregnancy. Moreover, a number of intermediates were uncovered along the basal-luminal progenitor cell axis, suggesting a continuum of alveolar-restricted progenitor states. Conclusions This extended single cell transcriptome atlas of mouse mammary epithelial cells provides the most complete coverage for mammary epithelial cells during morphogenesis to date. Together with chromatin accessibility analysis of TEB structures, it represents a valuable framework for understanding developmental decisions within the mouse mammary gland.

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