Single-Cell Examination Can Provide Insights into Tumor Microenvironment

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Cellular examination of follicular lymphoma reveals malignant B-cell types, coexpression of T-cell immune checkpoints.
Cellular examination of follicular lymphoma reveals malignant B-cell types, coexpression of T-cell immune checkpoints.

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.

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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.

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

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