The effects of chromosomal copy number variations (CNV) on transcriptional programs at single cell resolution in multiple myeloma

Chromosome copy number variations (CNV) are a near-universal feature of cancer however their specific effects on cellular function are poorly understood. Single-cell RNA sequencing (scRNA-seq) can reveal cellular gene expression however cannot directly link this to CNVs. Here we report scRNA-seq normalization methods that improve inter-cellular expression alignment, increasing the sensitivity of scRNA-seq for CNV detection. We additionally report sciCNV, a tool for inferring CNVs from scRNA-seq data. Together, these tools enable simultaneous profiling of DNA CNV and RNA within single cells. We apply these tools to multiple myeloma and examine the roles of pan cancer CNVs +8q and +1q. Cells with +8q23-24 upregulate MYC, MYC-target genes, mRNA translation, protein synthesis capacity and DEPTOR; and show reduced transcriptome size. Cells with +1q21-44 reconfigure translation to suppress unfolded protein stress and show increased proliferation, oxidative phosphorylation and MCL1. Overall, we report scRNA-seq methods that can reveal the function of CNVs in cancer. Single cell RNA-seq (10X Genomics) was used to profile the transcriptomes of plasma cells and B cells from the bone marrow of patients with multiple myeloma (MM). FACS was employed to enrich the profiled populations for the B cell - plasma cell lineage. Novel normalization methods (RTAM2) and single cell inferred copy number variation (sciCNV) methods were applied to the data to identify the effect of specific CNVs on transcriptional programs in MM cells. Normal plasma cells were identified by their expression of non-tumor immunoglobulin isotype and by their lack of tumor clone CNVs.