Extrachromosomal microDNA Signature as Candidate Biomarker in Pediatric Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Despite improved therapies, refractory and relapsed ALL remain the leading cause of cancer-related mortality in children. There is a need for accessible biomarkers for frequent, minimally invasive disease monitoring, and prompt intervention. MicroDNA is a novel extrachromosomal DNA that preferentially originates from the gene segments with high transcriptional activity and/or increased chromatin accessibility. We investigated whether microDNA-producing genes repertoire changes in a disease-dependent manner. We characterized microDNAs in 52 paired bone marrow (BM) and plasma samples from pediatric ALL patients at diagnosis, relapse, and remission. No difference in length or number of microDNA was noted across stages, but comparative analysis of microDNA profiles led to the identification of microDNA gene panel associated with active disease. The relative distribution of these genes was significantly different from that expected by chance (P <0.0001). Analyses of BM samples identified a signature comprising 289 distinct microDNA-producing genes present in multiple patients at diagnosis and relapse but absent in remission. The best biomarker candidates were 11 microDNA producing genes identified also in plasma samples at diagnosis and overrepresented in patients who relapsed (p=0.006). MicroDNA from the same genes was confirmed in relapse plasma samples. All signature genes are known to be involved in cancer proliferation or drug response. MicroDNA appears to be a candidate for a novel class of biomarkers for ALL, with the potential to improve precision diagnostics, particularly through their identification in plasma samples. Further validation in an independent cohort of patients is warranted.