Examining a large number of cells from a small number of patients with follicular lymphoma using single-cell RNA-seq (scRNA-seq) revealed a series of novel biological insights that could help identify new approaches for therapeutic development.

According to the study, complete isolation of the malignant B-cell population from a surgical biopsy is a significant challenge in follicular lymphoma, wrote authors. Using scRNA-seq, researchers were able to directly compare the transcriptomes of entirely normal and malignant B cells from the same biopsy.

The researchers analyzed 34,188 cells taken from 6 primary follicular lymphoma tumors. They compared gene expression between matched malignant and normal B cells from the same patients and identified a series of unique characteristics of the malignant cells including restricted immunoglobulin light chain expression, upregulation of the BCL2 gene, and downregulation of the FCER2, CD52, and MHC class II genes.

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By looking at thousands of these cells per patient tumor, the researchers identified a variety of malignant B-cell subclones that existed within follicular lymphoma, and classified characteristics of tumor-infiltrating T cells.

“Analysis of coexpression patterns within T-cell subsets identified novel candidate genes of T cell regulation that are consistently coexpressed with known immune checkpoint molecules,” the researchers wrote. “This included coexpression of CD59 – a potent inhibitor of signal transduction for T-cell activation – with both, TNFRSF18 and TNFRSF4, in CD4+ memory cells.”

Gene coexpressed with immune checkpoint molecules, such as CEBPA and B2M in Tregs, were also identified, “providing a better understanding of the gene networks involved in immune regulation.”

The amount of information gained through scRNA-seq “renders the technique an important tool if we are to understand the complex, intricate machinery responsible for a cancer’s immune evasion or response,” the researchers concluded.


  1. Andor N, Simonds EF, Czerwinski DK, et al. Single-cell RNA-Seq of lymphoma cancers reveals malignant B cell types and co-expression of T cell immune checkpoints. [published online December 27, 2018]. Blood. doi: 10.1182/blood-2018-08-862292