ArticleBriefings in functional genomics2022
Single-cell RNA sequencing analyses: interference by the genes that encode the B-cell and T-cell receptors.
Article in Briefings in functional genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
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- Persistence of mucosal CAR-T cells and inflammatory remodeling in enterocolitis associated with BCMA CAR-T cell therapy.Nature medicine · 2026Article
- A temporal map of B cell diversification mechanisms in mice.Nature immunology · 2026Article
- Viral load-driven systemic immune exhaustion is an enabler of antibody breadth in HIV infection.bioRxiv : the preprint server for biology · 2026Article
- CD8Nature · 2026Article
- Blood and tissue correlates of steroid non-response in checkpoint inhibition-induced immune-related adverse events.Communications medicine · 2025Article
- CD8medRxiv : the preprint server for health sciences · 2025Article
- CD226 identifies effector CD8Cell reports · 2025Article
- Prediction and characterisation of the human B cell response to a heterologous two-dose Ebola vaccine.Nature communications · 2025Article
- Epstein-Barr virus induces aberrant B cell migration and diapedesis via FAK-dependent chemotaxis pathways.Nature communications · 2025Article
- Development of ferret immune repertoire reference resources and single-cell-based high-throughput profiling assays.Journal of virology · 2025Article
- In vivo armed macrophages curb liver metastasis through tumor-reactive T-cell rejuvenation.Nature communications · 2025Article
- Impact of memory T cells on SARS-CoV-2 vaccine response in hematopoietic stem cell transplant.PloS one · 2025Article
- ClusterMatch aligns single-cell RNA-sequencing data at the multi-scale cluster level via stable matching.Bioinformatics (Oxford, England) · 2024Article
- Leveraging multi-omics data to empower quantitative systems pharmacology in immuno-oncology.Briefings in bioinformatics · 2024Article
- Characteristics and impact of infiltration of B-cells from systemic sclerosis patients in a 3D healthy skin model.Frontiers in immunology · 2024Article
- Interaction dynamics between innate and adaptive immune cells responding to SARS-CoV-2 vaccination in non-human primates.Nature communications · 2023Article
- Article
- Chronic antigen in solid tumors drives a distinct program of T cell residence.Science immunology · 2023Article
- Multi-omic analyses in immune cell development with lessons learned from T cell development.Frontiers in cell and developmental biology · 2023Review
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6 authors.
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Abstract
B and T cells are integral parts of the immune system and are implicated in many diseases, e.g. autoimmunity. Towards understanding the biology of B and T cells and subsets thereof, their transcriptomes can be analyzed using single-cell RNA sequencing. In some studies, the V(D)J transcripts encoding the variable regions of the B- and T-cell antigen receptors have been removed before the analyses. However, a systematic analysis of the effects of including versus excluding these genes is currently lacking. We have investigated the effects of these transcripts on unsupervised clustering and down-stream analyses of single-cell RNA sequencing data from B and T cells. We found that exclusion of the B-/T-cell receptor genes prior to unsupervised clustering resulted in clusters that represented biologically meaningful subsets, such as subsets of memory B and memory T cells. Furthermore, pseudo-time and trajectory inference analyses of early B-lineage cells resulted in a developmental pathway from progenitor to immature B cells. In contrast, when the B-/T-cell receptor genes were not removed, with the PCs used for clustering consisting of up to 70% V-genes, this resulted in some clusters being defined exclusively by V-gene segments. These did not represent biologically meaningful subsets; for instance in the early B-lineage cells, these clusters contained cells representing all developmental stages. Thus, in studies of B and T cells, to derive biologically meaningful results, it is imperative to remove the gene sequences that encode B- and T-cell receptors.
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