Single-Cell RNA Sequencing Reveals Compromised Immune Microenvironment in Precursor Stages of Multiple Myeloma
Authors: Zavidij Oksana , Haradhvala Nicholas , Mouhieddine Tarek H , Park Jihye , Pistofidis Romanos , Reidy Mairead , Huynh Daisy , Capelletti Marzia , Berrios Brianna , Rahmat Mahshid , Bustoros Mark , Liu Chia-Jen , He Meng Xiao , Maruvka Yosef , Rivotto Bradley , Hornburg Kalvis , Goldman Melissa , Van Allen Eliezer , McCarroll Steven A , Azzi Jamil , Getz Gad , Ghobrial Irene M. 
Published: October 2019

Abstract
Introduction: In multiple myeloma (MM), despite well-characterized precursor states such as monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM), there is a lack of sufficient biomarkers to predict mechanisms of disease progression. Most genomic analyses have sought biomarkers by study of the malignant plasma cells, however, cancers form a complex ecosystem with the immune and stromal microenvironment. Thus, to characterize the cellular composition and transcriptional programs of each component of the tumor and microenvironment at different stages of MM progression, we employed a single-cell RNA sequencing on a cohort of 22 patients and 9 healthy donors.
Methods: We performed 10X droplet-based single-cell RNA sequencing using CD138-expressing plasma cells and microenvironmental populations isolated from bone marrow (BM) aspirates of patients with MGUS (n=6), low-risk SMM (n=3), high-risk SMM (n=13), newly diagnosed MM (n=8) and from 9 healthy donors (NBM). We collected a total of ~88.8K cells, comprising ~48K CD138+ cells (~36.4 from MM stages) and ~40.8K CD45+/CD138- cells (~30.8 from MM stages).Raw read data was processed using the Cell Ranger pipeline to obtain a gene-by-cell expression matrix, which was used to identify cell types and transcriptional programs by clustering and non-negative matrix factorization.
Results: Expression profiles of plasma cells revealed clear tumor-specific differences including known oncogenic drivers in MM (MMSET/FGFR3, CCND1 and MAFB) as well as Lysosome-associated Membrane Protein 5 (LAMP5),Histone Cluster 1 H1 Family Member C (HIST1H1C) and Amphiregulin (AREG) distinguishing them from healthy plasma cells. We identified a subset of cycling plasma cells, observing a range of proliferative activity of the malignant fraction. Furthermore, our approach allowed a unique head-to-head comparison of gene expression changes in normal and malignant plasma cells in the MGUS and SMM patients within an individual, excluding inter-individual variation. We were able to discriminate malignant from non-malignant plasma cells and identify transcriptional alterations including known drivers, genes related to immune modulation (NKBIA) or controlling transcription and differentiation (EID1).Some alterations were patient-specific, while others, such as MHC I overexpression and CD27 loss, were recurrently observed across subsets of the cohort.
Analysis of BM microenvironment in several stages of MM progression demonstrated a striking shift in the composition of immune cells with significant infiltration of natural killer cells, non-classical monocytes/macrophages, and T cells, enriched even in the earliest stages of the disease. Further investigation revealed significant upregulation of HLA expression at the mRNA level in CD14+ monocytes/macrophages. Intriguingly, comparison of healthy and patient samples by CyTOF showed downregulation of surface MHC II representation in the corresponding cell type, and moreover, co-culture with MM cell lines induced a sharp decrease of extracellular MHC II. This provided strong evidence for compromised antigen presentation by macrophages in the disease setting, hinting at a mechanism of immune evasion. Additionally, expression signatures in cytotoxic T-cells indicated a substantial skewing towards either granzyme B/H- or granzyme K-expressing memory cell-like transcriptional program. In a subgroup of patients, we found a strong simultaneous enrichment of the anti-viral/anti-bacterial gene expression signature for interferon type-1 activated genes in CD14+ monocytes/macrophages and T cells.
Together, our results provide a comprehensive view at the complex interplay of the immune and malignant cells in different stages of the disease. We, for the first time, demonstrate the immune response beginning in premalignant conditions to be heterogeneous, including compromised antigen presentation as well as alterations in cellular composition and signaling. Consideration of the type of immunological response may prove valuable in determination of progression risk, as well as open up potential strategies for therapy.

Disclosures
Bustoros: Dava Oncology: Honoraria. Ghobrial:Celgene: Consultancy; Janssen: Consultancy; BMS: Consultancy; Takeda: Consultancy.