scRNA-Seq Reveals Lymphoma B Cell Diversity and T Cell Immune Checkpoint Co-Expression

Follicular lymphoma (FL) is a generally incurable B-cell malignancy which has the potential to transform into highly aggressive lymphomas. Genomic studies indicate it is often a small subpopulation rather than the dominant population in the FL that gives rise to the more aggressive subtype. To resolve the underlying transcriptional networks of follicular B-cell lymphomas at single molecule and cell resolution, we leveraged droplet-based barcoding technology for highly parallel single cell RNA-Seq. We analyzed the transcriptomes from tens of thousands of cells derived from five primary FL tumors. Simultaneously, we conducted multi-dimensional flow cell sorting to validate our characterizing of cellular lineages and critical expressed proteins. For each tumor, we identified multiple cellular subpopulations, matching known hematopoietic lineages. Comparison of gene expression by matched malignant and normal B cells from the same patient revealed tumor-specific features. Malignant B cells exhibited restricted immunoglobulin light chain expression (either Ig Kappa or Ig Lambda), as well the expected upregulation of the BCL2 gene, but also down-regulation of the FCER2, CD52 and MHC class II genes. By leveraging the single-cell resolution on large numbers of cells per patient, we were able to examine tumor-resident T cells. We identified pairs of immune checkpoint molecules that were co-expressed, providing a potentially useful strategy for selection of patient-tailored combination immunotherapies. In summary, massively parallel measurement of single-cell expression in thousands of tumor cells and tumor-resident lymphocytes can be used to obtain a systems-level view of the tumor microenvironment and identify new avenues for therapeutic development.]]> Inclusion criteria for cases (lymphoma patients): >18 years of age Diagnosis of non-Hodgkin's lymphoma or Hodgkin's disease, or any solid tumor, where standard of care procedure for tissue collection is planned (i.e. lymph node biopsy, FNA, core needle biopsy, skin punch biopsy, bone marrow biopsy, apheresis, splenectomy) and/or the patient has agreed to an additional biopsy or blood sample in addition to routine pathology For lymphoma or solid tumor patients who do not have a diagnostic tumor tissue collection planned, availability of archival tumor tissue block or unstained slides. Provide informed consent Inclusion criteria for "healthy control" population: Diagnosis of non-cancer related surgical indication for lymph node(s) resection. Provide informed consent Exclusion criteria: not applicable ]]> 9/1987 to 1/2003: Specimen collection 12/2015: Sequencing of first batch 03/2016: Sequencing of second batch 07/2016: Sequencing of third batch 05/2017: End of study ]]>