Integrated genomic Sequencing in Myeloid Blast Crisis Chronic Myeloid Leukemia (MBC-CML), identified potentially important findings in the context of leukemogenesis model

Background Chronic myeloid leukemia (CML) is a model of leukemogenesis in which the exact molecular mechanisms underlying blast crisis still remained unexplored. Using integrated genomic sequencing, this study detected multiple common and rare important findings in myeloid blast crisis CML (MBC-CML) which involved all classes of genes important in the leukemogenesis model. Methods: Integrated genomic sequencing through Whole Exome Sequencing (WES), Chromosome-seq and RNA-sequencing were conducted on the peripheral blood samples of three CML patients in the myeloid blast crisis. An in-house filtering pipeline was applied to assess important variants in cancer-related genes. AMP and ACMG guidelines were used for the interpretation of potentially important findings (PIFs) and potentially actionable findings (PAFs). Results: Single nucleotide variation (SNV) and small InDel analysis by WES detected sixteen PIFs which affect all five known classes of leukemogenic genes in myeloid malignancies including signaling pathway components (ABL1, PIK3CB, PTPN11), transcription factors (GATA2, PHF6, IKZF1, WT1), epigenetic regulators (ASXL1), tumor suppressor and DNA repair genes (BRCA2, ATM, CHEK2) and components of the spliceosome (PRPF8). These variants affect genes which may affect the p, self-renewal and differentiation of leukemia stem cells (LSCs). Patients No.1 and No.2 both had actionable known missense variants on ABL1 (p.Y272H, p.F359V) and frameshift variants on ASXL1 (p.A627Gfs*8, p.G646Wfs*12). The GATA2-L359S in the patient No.1, PTPN11-G503V and IKZF1-R208Q variants in the patient No.3 were also PAFs. All detected variants were confirmed in RNA-sequencing. Copy number variation (CNV) analysis by chromosome-seq in the patient No. 3 detected several pathogenic deletions in the short and long arms of chromosome 7 involved at least three important leukemogenic genes (IKZF1, EZH2, and CUX1). The detected large deletion in the short arm of chromosome 17 in the patient No. 2 also resulted in deletion of the TP53 gene. Conclusion: The integrated genomic sequencing along with RNA-sequencing can effectively detect and confirm large spectrum of variants from SNVs to CNVs. This strategy may be an efficacious method to identify actionable findings and to understand the pathophysiological mechanisms underlying MBC-CML and may provide further insights into the MBC-CML genetic basis and its management in future.