EFB Dengue Literature Review

Single-Cell RNA Sequencing

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Single-Cell RNA Sequencing

Overview

Single-cell RNA sequencing (scRNA-seq) enables transcriptomic profiling at single-cell resolution, allowing identification of cell states, subtypes, and developmental trajectories within heterogeneous populations. When paired with single-cell TCR or BCR sequencing (e.g., 10x Genomics 5’ V(D)J), it enables simultaneous characterisation of gene expression and antigen receptor clonality.

Key Points from Literature

  • scRNA-seq + scTCR-seq of activated CD4⁺ T cells in dengue: Ansari2025 performed 10x Genomics Chromium 5’ scRNA-seq + scTCR-seq on FACS-sorted CD38⁺HLA-DR⁺ CD4⁺ T cells from 4 acute dengue patients (4,361 cells total). This identified: (1) CXCR5⁺ Tfh-like cluster, (2) IL-21⁺ helper Tph, (3) GZMB⁺ cytotoxic Tph, and (4) regulatory/exhausted populations. Paired TCR data showed largely distinct clonotype usage between helper and cytotoxic Tph (only 13 shared clonotypes) (see Ansari2025 - Peripheral T Helper Subset Drives B Cell Response in Dengue, n=4 patients).
  • Distinction from bulk RNA-seq: Prior studies in this wiki used bulk RNA-seq of sorted B cell populations (e.g., Jenks2018 - DN2 B Cells and EF Pathway in SLE — 2,154 DEGs across B cell subsets; Scharer2019 - Epigenetic Programming in SLE B Cells — 5,090 DEGs). scRNA-seq complements these by resolving heterogeneity within sorted populations but has lower per-cell gene detection sensitivity.
  • 10x Genomics platform: The 10x Chromium system used in Ansari2025 is the same platform used for scV(D)J BCR sequencing in Woodruff2020 (ASC repertoire in COVID-19). The 5’ chemistry enables simultaneous gene expression + TCR/BCR sequencing from the same cell (see BCR Sequencing for the BCR application).
  • LANDMARK B CELL scRNA-seq — defining the alternative lineage (Sutton2021): Two complementary scRNA-seq platforms applied to B cells from malaria-exposed and non-exposed donors: (1) Smart-seq2 (plate-based, full-length mRNA): 163 Pf-tetramer⁺ B cells from 11 donors (3 malaria-exposed, 8 non-exposed), providing full-length BCR sequences for SHM quantification and V gene usage analysis. (2) 10x Chromium 3’ (droplet-based): >12,000 total B cells from 4 donors (2 malaria-exposed Kenyan adults + 2 non-exposed Australian donors), providing high-throughput unbiased clustering. Combined with CITE-seq surface protein measurement (CD11c, CXCR3, CD21, CD27), this identified 9 transcriptomic clusters separated into two developmental branches — an “alternative lineage” (atBC1, atBC2, atBC3, MBC1) defined by TBX21, ITGAX, FCRL5, and a “classical lineage” (MBC2, MBC3, actBC). Pseudotime analysis (Slingshot) placed these on separate trajectories from naive B cells. This is the most comprehensive scRNA-seq characterisation of the T-bet⁺/CD11c⁺ B cell population to date (see Sutton2021 - Alternative Lineage B Cells in Vaccination and Infection, 4 cohorts).

Contradictions & Debates

None documented in current wiki sources.

RNA Sequencing, BCR Sequencing, FACS Sorting, Peripheral Helper T Cell, CITE-seq

Sources

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