Abstract LB-012: Single cell RNA-sequencing of multiple myeloma clinical patients for identifying novel immuno-oncology drug targets
Authors: Kumar Namit , Peterson Vanessa M. , Zhang Kelvin X. , Li Lixia , Garrett-Engele Philip W. , Moniz Raymond J. , Klappenbach Joel A. 
Published: August 2018

Recent advances in single cell genomic technologies have enabled unbiased quantification of cellular states within complex tissues, mechanisms of differentiation, biomarker presentation in cellular subsets; yet their applications in evaluating the response to therapeutic interventions are still underexplored. In our study, we apply single cell RNA sequencing (scRNA-seq) to uncover mechanisms and drug targets for Multiple Myeloma(MM), a malignancy of plasma cells with estimates of 30,770 new cases and 12,770 deaths in 2018 within US alone.

Using the 10x Genomics scRNA-seq platform, we profiled ten clinical MM patients, pre- and post-treatment with four standard of care chemotherapy regimens (VAD, VCD, VMP, MP; A=Adriamycin; C=Cyclophosphamide; D=Dexamethasone; M=Melphalan; P=Prednisone; V=Velcade). We sequenced a total of 106,000 cells and determined differential gene expression upon treatment at single-cell resolution comparing 37,926 pre- vs 44,842 post-treatment cells.

We identify activation of immune cells with increased expression of IL1B, CD14, CD52, CCL4, IFITM3, PSMA4; and repression of translational machinery with reduced expression of PABPC1, PABPC4, FUS, POLR2A in post-treatment (abs(log2 FC &gt;0.25) and P-value &lt; 10-5). To understand the functional implication of gene expression changes, we identified that the upregulated genes are enriched for ontologies regulating protein ubiquitination pathway, communication between innate and adaptive immune cells, TREM1 signaling, dendritic cell maturation (P-value 3.16x10-17, 3.47x10-7, 3.09 x10-5, 4.07x10-5 respectively). Downregulated genes are enriched for EIF2 signaling, regulation of eIF4 and p70S6K signaling, mTOR signaling (P-value 3.16x10-13, 1.86x10-8, 2.24x10-6 respectively). Additionally, we performed a comparative analysis of differentially expressed genes in response to each drug regimen. We identified genes upregulated upon MP drug regimen are comparatively enriched for IL-8 signaling, while treatment with VMP enhances B-cell receptor signaling (P-value 5.5x10-12 and 9.0x10-9 respectively). Further, we have used our unbiased transcriptomic interrogation of MM clinical patients to identify a panel of 100+ biomarkers that are being evaluated at a proteomics level using our recently developed technique, RNA Expression and Protein sequencing (REAP-seq). This method enables us to obtain readout for whole transcriptome and proteins (&gt;100) using oligo conjugated antibodies while retaining single cell resolution. Transcriptome and/or proteome analysis of bulk tumor often fails to detect signature of rare cell populations. Our study here highlights the use of single cell readouts for identifying novel oncology mechanisms, drug targets and drug combinations for more efficacious immunotherapies.

Citation Format: Namit Kumar, Vanessa M. Peterson, Kelvin X. Zhang, Lixia Li, Philip W. Garrett-Engele, Raymond J. Moniz, Joel A. Klappenbach. Single cell RNA-sequencing of multiple myeloma clinical patients for identifying novel immuno-oncology drug targets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-012.