Single-cell RNA-Seq of follicular lymphoma reveals malignant B-cell types and coexpression of T-cell immune checkpoints

Blood. 2019 Mar 7;133(10):1119-1129. doi: 10.1182/blood-2018-08-862292. Epub 2018 Dec 27.


Follicular lymphoma (FL) is a low-grade B-cell malignancy that transforms into a highly aggressive and lethal disease at a rate of 2% per year. Perfect isolation of the malignant B-cell population from a surgical biopsy is a significant challenge, masking important FL biology, such as immune checkpoint coexpression patterns. To resolve the underlying transcriptional networks of follicular B-cell lymphomas, we analyzed the transcriptomes of 34 188 cells derived from 6 primary FL tumors. For each tumor, we identified normal immune subpopulations and malignant B cells, based on gene expression. We used multicolor flow cytometry analysis of the same tumors to confirm our assignments of cellular lineages and validate our predictions of expressed proteins. Comparison of gene expression between matched malignant and normal B cells from the same patient revealed tumor-specific features. Malignant B cells exhibited restricted immunoglobulin (Ig) light chain expression (either Igκ or Igλ), as well the expected upregulation of the BCL2 gene, but also downregulation of the FCER2, CD52, and major histocompatibility complex class II genes. By analyzing thousands of individual cells per patient tumor, we identified the mosaic of malignant B-cell subclones that coexist within a FL and examined the characteristics of tumor-infiltrating T cells. We identified genes coexpressed with immune checkpoint molecules, such as CEBPA and B2M in regulatory T (Treg) cells, providing a better understanding of the gene networks involved in immune regulation. In summary, parallel measurement of single-cell expression in thousands of tumor cells and tumor-infiltrating lymphocytes can be used to obtain a systems-level view of the tumor microenvironment and identify new avenues for therapeutic development.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biopsy
  • CCAAT-Enhancer-Binding Proteins / genetics
  • CD4-Positive T-Lymphocytes / cytology
  • CD52 Antigen / genetics
  • Cell Lineage
  • Flow Cytometry
  • Gene Expression Profiling
  • Gene Expression Regulation, Leukemic
  • Hematopoietic Stem Cells / cytology
  • Histocompatibility Antigens Class II / metabolism
  • Humans
  • Immune System
  • Immunoglobulin G
  • Lectins, C-Type / genetics
  • Leukocytes, Mononuclear / cytology
  • Lymphoma, B-Cell / blood
  • Lymphoma, B-Cell / genetics*
  • Lymphoma, Follicular / blood
  • Lymphoma, Follicular / genetics*
  • Palatine Tonsil / metabolism
  • Receptors, IgE / genetics
  • Sequence Analysis, RNA
  • T-Lymphocytes, Regulatory / cytology*
  • Transcriptome
  • Tumor Microenvironment
  • beta 2-Microglobulin / genetics


  • B2M protein, human
  • CCAAT-Enhancer-Binding Proteins
  • CD52 Antigen
  • CD52 protein, human
  • CEBPA protein, human
  • FCER2 protein, human
  • Histocompatibility Antigens Class II
  • Immunoglobulin G
  • Lectins, C-Type
  • Receptors, IgE
  • beta 2-Microglobulin