Comprehensive Genetic Interrogation of Circulating Multiple Myeloma Cells at Single Cell Resolution

Continuous genomic evolution has been a major limitation to curative treatment of multiple myeloma (MM). Frequent monitoring of the genetic heterogeneity in MM from blood, rather than serial bone marrow (BM) biopsies, would therefore be desirable. We hypothesized that genomic characterization of circulating MM cells (CMMCs) recapitulates the genetics of MM in BM biopsies, enables MM classification, and is feasible in the majority of MM patients with active disease.

Methods: To test these hypotheses, we developed a method to enrich, purify and isolate single CMMCs with a sensitivity of at least 1:10(5). We then performed DNA- and RNA-sequencing of single CMMCs and compared them to single BM-derived MM cells. We determined CMMC numbers in 24 randomly selected MM patient samples and compared them to numbers of circulating MM cells obtained by flow cytometry. We performed single-cell whole genome amplification of single cells from 10 MM patients, and targeted sequencing of the 35 most recurrently mutated loci in MM. A total of 568 single primary cells representing CMMCs, BM MM cells, CD19⁺ B lymphocytes, CD45⁺CD138^- WBC from these patients were subjected to DNA-sequencing. By processing 80 single cells from four MM cell lines with known mutations we determined the mean sensitivity of mutation detection in single cells to be 93 ± 9%. In addition to DNA-sequencing we also isolated 57 single MM cells from the BM and peripheral blood of two MM patients and performed whole transcriptome single cell RNA-sequencing.

Results: In 24 randomly selected MM patient samples we detected >12 CMMCs per 1ml of blood in all 24 patients. In comparison, by flow cytometry, we detected ≥10 CMMCs per 10(5) white blood cells in 10/24 cases (42%), ≥1 CMMC but ≤ 10 CMMCs in 13/24 cases (54%), and < 1 CTCs in 1/24 patients (4%). Mutational analysis of 35 recurrently mutated loci in 335 high quality single MM cells from the blood and BM of 10 patients, including one MGUS patient, revealed the presence of a total of 12 mutations (in KRAS, NRAS, BRAF, IRF4 and TP53). All targeted mutations that were detected by clinical-grade genotyping of bulk BM were also detected in single cell analysis of CMMCs. While in most patients, the fraction of mutated single cells was similar between blood and BM, in three patients, the proportion of MM cells harboring TP53 R273C, BRAF G469A and NRAS G13D mutations was significantly higher in the blood than in the BM, suggesting a different clonal composition. We developed an analytical model to predict whether a genetic locus underwent loss of heterozygosity, using the distribution of known allelic fractions of previously described mutations in MM cell lines as a benchmark. In two patients who simultaneously harbored two mutations, we predicted a BRAF G469E and a KRAS G12C mutation to be heterozygous, whereas the loci harboring a TP53 R273C and a TP53 R280T mutation were predicted to be associated with LOH with high statistical confidence. Whole transcriptome single cell RNA-sequencing of 57 MM cells from the BM and peripheral blood of two patients showed >3,700 transcripts per cell. Single-cell RNA-sequencing allowed for a clear distinction between normal plasma cells and MM cells, either based on analysis of CD45, CD27, and CD56 alone, or by unsupervised hierarchical clustering of detected transcripts in single cells. In addition, single cell CMMC expression analysis could be used to infer the existence of key MM chromosomal translocations. For example, CCND1 and CCND3 were highly upregulated in single MM cells from the blood and BM of two patients, whose MM was found by FISH analysis to harbor a t(11;14) and a t(6;14) translocation, respectively.

Conclusion: We demonstrate that extensive genomic characterization of MM is feasible from very small numbers of CMMCs with single cell resolution. Interrogation of single CMMCs faithfully reproduces the pattern of somatic mutations present in MM in the BM, identifies actionable oncogenes, and reveals if somatic mutated loci underwent loss of heterozygosity. Single CMMCs also reveal mutations that are not detectable in the BM either by single cell sequencing or clinical grade bulk sequencing. Single cell RNA-sequencing of CMMCs provides robust transcriptomic profiling, allowing for class-differentiation and inference of translocations in MM patients.