Liquid Biopsy-Derived DNA Sources as Tools for Comprehensive Mutation Profiling in Multiple Myeloma: A Comparative Study

SIMPLE SUMMARY: Multiple myeloma (MM) is characterized by an expansion of plasma cells in the bone marrow (BM). The genetics of MM are highly complex with multiple mutations and genetic subpopulations of tumor cells that arise during the disease evolution, affecting prognosis and treatment response. Standard bone marrow DNA analysis requires an invasive sample collection and does not always reflect the complete mutation profile. Therefore, we examined the possibility to use peripheral blood-based liquid biopsies as an alternative DNA source for mutation profiling. By comparing DNA from circulating tumor cells with circulating tumor-derived vesicles and cell-free DNA (cfDNA), we found that the latter provided the best concordance with bone marrow DNA and also showed mutations derived from myeloma cell populations that were undetectable in bone marrow. Our comparative study indicates that cfDNA is the preferable circulating biomarker for genetic characterization in MM and can provide additional information compared to standard BM analysis. ABSTRACT: The analysis of bone marrow (BM) samples in multiple myeloma (MM) patients can lead to the underestimation of the genetic heterogeneity within the tumor. Blood-derived liquid biopsies may provide a more comprehensive approach to genetic characterization. However, no thorough comparison between the currently available circulating biomarkers as tools for mutation profiling in MM has been published yet and the use of extracellular vesicle-derived DNA for this purpose in MM has not yet been investigated. Therefore, we collected BM aspirates and blood samples in 30 patients with active MM to isolate five different DNA types, i.e., cfDNA, EV-DNA, BM-DNA and DNA isolated from peripheral blood mononucleated cells (PBMNCs-DNA) and circulating tumor cells (CTC-DNA). DNA was analyzed for genetic variants with targeted gene sequencing using a 165-gene panel. After data filtering, 87 somatic and 39 germline variants were detected among the 149 DNA samples used for sequencing. cfDNA showed the highest concordance with the mutation profile observed in BM-DNA and outperformed EV-DNA, CTC-DNA and PBMNCs-DNA. Of note, 16% of all the somatic variants were only detectable in circulating biomarkers. Based on our analysis, cfDNA is the preferable circulating biomarker for genetic characterization in MM and its combined use with BM-DNA allows for comprehensive mutation profiling in MM.