Extrachromosomal circular DNA of multiple myeloma

Background: Extrachromosomal circular DNA (EccDNA) is widespread in various heterogeneous tumors and closely associated with tumor resistance and progression. Methods: Circle-seq and mRNA-seq were done on samples from three multiple myeloma (MM) patients, one when they had a complete response and one when they relapsed. Results: A large number of EccDNA molecules were detected with high heterogeneity among the six samples. Circle-seq combined with mRNA-seq analyses revealed that there is no linear relationship between mRNA expression and EccDNA quantity. Chromosome 19 presented the highest density of differentially expressed EccDNA genes, followed by chromosome 17. Only the T3 sample showed del(17p) by fluorescence in situ hybridization at the time of relapse. Approximately 92% of all upregulated EccDNA genes from chromosome 17 (137) were present in the T3 sample. By integrating Circle-seq and mRNA-seq data, we obtained several potentially functional candidate protein-coding genes and miRNAs from chromosome 17. We further assessed the prognostic value of the three protein-coding genes in the MMRF-COMPASS clinical trial and found that all three genes were poor prognostic indicators for MM. Furthermore, WB, CCK8 and Annexin V-FITC/PI assays revealed that the overexpression of 2',3'-cyclic nucleotide 3' phosphodiesterase (CNP) downregulated the apoptotic pathway and increased bortezomib tolerance in MM cells. Conclusion: We performed a Circle-seq analysis of MM and investigated the heterogeneity of EccDNA. Analysis of data from clinical studies and basic experiments revealed that the gene carried on EccDNA most likely contributed to the increased tolerance of bortezomib in MM with del(17p).