Distinguishing cell–cell complexes from dual lineage cells using single‐cell transcriptomics is not trivial

Abstract

In their recent correspondence, Jie et al. strongly defend that the DE cell population they discovered are always dual lineage co-expressing cells and not complexes of B cells and T cells, which we have previously described as frequently present in singlecell RNA sequencing data. Here, we respond to the specific arguments made in their correspondence. Specifically, we demonstrate that the presence of a gene signature in a given cell population is not enough to ascertain that it does not contain cell-cell complexes, or that it represents a biologically distinct cell type. We also show that the gene signature of DE cells contains several genes from the myeloid lineage, suggesting either that their DE cells are a triple-lineage co-expressing cell, or a threecomponent cell aggregate. Finally, we identify multiple transcriptomic features of DE cells that correspond to B cell-T cell complexes, namely the presence of lower average expression of B-and T-cell specific genes, and a higher number of detected genes per cell. Taken together, our results demonstrate that solely based on their scRNAseq profile, it is not possible to ascertain that DE cells are dual expressing cells and not cell-cell complexes.We have recently discovered that cell-cell doublet populations pairing a T cell and an antigen-presenting cell (APC)-such as a monocyte or a B cell-can be detected in the singlet gate of ex vivo human blood samples analyzed by flow cytometry [1,2]. Strikingly, the T cell-

Striking an alliance between T cells and macrophages for enhanced cancer immunotherapy

“…Another, more technical, phenomenon that this paper provides clarity on is the identity of macrophage/T‐cell‐like clusters that may be familiar to practitioners of single‐cell sequencing on immune compartments. Containing both CD14 and CD3 transcripts, these cells have been previously identified as doublets, dual‐cell complexes or even “dual lineage cells” 9 . However, this paper strongly suggests the population actually represents macrophage‐engulfed T cells.…”

“…Containing both CD14 and CD3 transcripts, these cells have been previously identified as doublets, dual-cell complexes or even "dual lineage cells". 9 However, this paper strongly suggests the population actually represents macrophage-engulfed T cells.…”

mastR: Marker Automated Screening Tool for multi-omics data

“…While not explicitly discussed, in some marker identification studies, the presence of two or more closely related groups in the data may pose challenges for the identified markers to be effective in distinguishing these groups (Burel, et al, 2022). In such cases, mastR allows the preservation of the top features from specific DE comparisons for further refinement and performing rank product scoring by utilizing the underlying statistics (e.g., logFC, adjusted p values).…”