Single Cell Multi-Omic Profiling of Multiple Myeloma with t(4;14) Finds an Immune Microenvironment Gene Signature That Correlates with Clinical Outcomes

Background Multiple Myeloma (MM) is an incurable plasma cell (PC) malignancy and high risk MM remains an unmet clinical need. Translocation 4;14 occurs in 15% of MM and is associated with an adverse prognosis. A deeper understanding of the biology and immune micro-environment of t(4;14) MM is necessary for the development of effective targeted therapies. Single Cell multi-omics provides a new tool for phenotypic characterization of MM. Here we used Proteona's ESCAPE™ single cell multi-omics platform to study a cohort of patients with t(4;14) MM. Methods Diagnostic bone marrow (BM) samples from 13 patients with t(4;14) MM (one of whom had samples at diagnosis and relapse) were analysed using the ESCAPE™ platform from Proteona which simultaneously measures gene and cell surface protein expression of 65 proteins in single cells. Cryopreserved BM samples were stained with antibodies and subsequently sorted on CD138 expression. The CD138 positive and negative fractions were recombined at a 1:1 ratio for analysis using the 10x Genomics 3' RNAseq kit. Resulting data were analyzed with Proteona's MapSuite™ single cell analytics platform. In particular, Mapcell was used to annotate the cells and MapBatch was used for batch normalization in order to preserve rare cell populations. Results Patients had a median age of 63 years and received novel agent-based induction. Median progression free and overall survival (PFS and OS) were 22 and 34 months respectively. We first analyzed serial BM samples from an individual patient that were taken at diagnosis and relapse following bortezomib based treatment. The PCs in this patient showed variations in gene expression between diagnosis and relapse (Fig 1A), including the reduction of HIST1H2BG expression, which has previously been correlated with resistance to bortezomib. Subsequent analysis of the immune cells identified a shift in the ratio of T cells to CD14 monocytes from 5.7 at diagnosis to 0.6 at relapse suggesting a major change in the BM immune micro-environment in response to therapy. Next, we analyzed the malignant PCs of the diagnostic samples. As expected, MMSET (NSD2) was overexpressed in all PCs compared to normal PCs, while FGFR3 expression could be categorized into no expression of FGFR3, low expression (80% of cells expressing FGFR3) (Fig 1B). No gene or protein expression patterns within the PCs were identified that correlated with PFS or OS in this cohort