Abstract 3693: Single cell RNA-Seq of primary lymphomas reveals the diverse transcriptional states of the cancer immunologic milieu
Authors: Andor Noemi , Simonds Erin , Chen Jiamin , Wood Christina , Grimes Susan , Czerwinski Debra , Zheng Grace , Levy Ronald , Ji Hanlee P. 
Published: July 2017

Abstract
Follicular lymphoma (FL) is an incurable B-cell malignancy that has the potential to transform into highly aggressive, lethal lymphomas. To resolve the cellular characteristics of the underlying cancer immunologic milieu at single cell resolution, we leveraged droplet-based barcoding technology for highly parallel single cell RNA-Seq. We analyzed the transcriptomes across tens of thousands of indviidual cells derived from five primary FL tumors (average &gt; 5,000 cells per sample). These tumors were obtained via direct surgical biopsies. In parallel, we conducted multi-dimensional flow cytometry that orthogonally confirmed our characterization of the various cell types including the various subsets of T cells that existed within each tumor. We identified multiple cellular subpopulations, matching known hematopoietic lineages that were present within each tumor. Despite some common features, such as MYC and BCL overexpression, transcriptional patterns and regulatory programs destinguished the different tumors from each other. We compared the transcriptional profiles of malignant cellular subpopulations to the matched normal B-cells within each sample. Malignant B-cells were characterized by expression of restricted immunoglobulin light chain type (either kappa or lambda), BCL2 expression, and CD20 expression. In each case a minor population of normal B-cells was characterized by expression of the opposite light chain type and a pattern of gene expression common to B cells in all tumor samples and normal peripheral blood. Tumor B cells consistently demonstrated downregulation of β-2-microglobulin and for those cases that harbored a founder CREBBP mutation, a downregulation of MHC II, that would cause an alteration in antigen presentation and evasion of the T cell immune system. Moreover, we characterized the transcriptional profiles of the infiltrating T-cell populations within each tumor, providing a high-resolution perspective of immunologic cellular interactions. Overall, we identified the diverse transcriptional states at single cell resolution among different tumors and discovered specific genes that were aberrantly expressed compared to normal B cells within the same microenvironment. Our findings provide an unprecedented resolution of distinct immune lineages as seen by transcriptionally characterized cell diversity. Studies using single cell genomics may have implications for considering immunotherapeutic efficacy.
Citation Format: Noemi Andor, Erin Simonds, Jiamin Chen, Christina Wood, Susan Grimes, Debra Czerwinski, Grace Zheng, Ronald Levy, Hanlee P. Ji. Single cell RNA-Seq of primary lymphomas reveals the diverse transcriptional states of the cancer immunologic milieu [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3693. doi:10.1158/1538-7445.AM2017-3693