Molecular and cytogenetic characterization of myelodysplastic syndromes in cell-free DNA

Abstract

Molecular and cytogenetic studies are essential in patients with myelodysplastic syndromes (MDS) for diagnosis and prognosis. Cell-free DNA (cfDNA) analysis has been reported as a reliable non-invasive approach for detecting molecular abnormalities in MDS, however, there is limited information about cytogenetic alterations and monitoring in cfDNA. We have assessed the molecular and cytogenetic profile of a cohort of 70 patients with MDS by next-generation sequencing (NGS) using cfDNA and compared the results to paired bone marrow (BM) DNA. Sequencing of BM DNA and cfDNA showed a comparable mutational profile (92.1% concordance) and variant allele frequencies (VAF) strongly correlated between both sample types. Of note, SF3B1 mutations were detected with significantly higher VAF in cfDNA than in BM DNA. NGS and microarrays were highly concordant to detect chromosomal alterations although with lower sensitivity than karyotype/FISH. Nevertheless, all cytogenetic aberrations detected by NGS in BM DNA were also detected in cfDNA. Additionally, molecular and cytogenetic alterations were monitored and we observed an excellent correlation between the VAF of mutations in BM DNA and cfDNA across multiple matched time points. A decrease in the cfDNA VAF was detected in patients responding to therapy, but not in non-responding patients. Of note, cfDNA analysis also showed cytogenetic evolution in 2 cases not responding to treatment. In conclusion, although further studies with larger cohorts are required, our results support the analysis of cfDNA as a promising strategy for performing molecular characterization, detection of chromosomal aberrations and monitoring of MDS patients.

High cell-free DNA is associated with disease progression, inflammasome activation and elevated levels of inflammasome-related cytokine IL-18 in patients with myelofibrosis

“…Exacerbated proliferation and turn-over of the MPN clone leading to systemic DNA leakage is a plausible explanation, supported by the relationship between cfDNA and tumor burden parameters. Moreover, ineffective hematopoiesis, which characterizes cytopenic MF, could be regarded as a contributing factor, as suggested by the association between cfDNA and both anemia and thrombocytopenia, bearing comparison with the increase in cfDNA described in patients with myelodysplastic syndromes ( 49 ). In addition, pyroptosis, which is an inflammatory type of cell death mediated by inflammasome-induced Gasdermin D activation and membrane pore formation ( 26 ), might represent another potential mechanism.…”

Prevalence of massively diluted bone marrow cell samples aspirated from patients with myelodysplastic syndromes (MDS) or suspected of MDS: A retrospective analysis of nationwide samples in Japan

“…Studies have reported that gene analysis data are very similar between blood samples and BM samples. 24,25 However, the degree of haemodilution in BM samples is vital for interpreting such data.…”

“…In addition, if diagnostic tests not affected by the BM haemodilution are developed, they will be valuable. Studies have reported that gene analysis data are very similar between blood samples and BM samples 24,25 . However, the degree of haemodilution in BM samples is vital for interpreting such data.…”

Liquid biopsy in hematological malignancies: current and future applications

“…NGS on ctDNA and microarrays were highly concordant in detecting chromosomal alterations, and all cytogenetic aberrations detected by NGS in BM DNA were also detected on ctDNA. These results suggest that the analysis of ctDNA is a promising strategy for performing molecular characterization and monitoring of patients with MDS ( 81 ).…”