3.1 novel fusion gene PIEZO1::CBFA2T3 is associated with dysregulation of CBFA2T3
Whole transcriptome RNA sequencing (RNA-Seq) performed on the patient’s bone marrow sample detected a highly likely pathogenic fusion genes, PIEZO1 exon1::CBFA2T3 exon2 (figure 1A). The novel PIEZO1::CBFA2T3 fusion in this elderly male patient preserved the coding region of all functional domains of CBFA2T3, possibly acts as a driver in oncogenesis (Fig. 1A). To elucidate the pathogenic significance of PIEZO1::CBFA2T3, we screened four CBFA2T3-coexpressing genes in AML based on a previous study (up-regulating genes include CDKN1A, JUP, KAT2A, and the down-regulating gene TYROBP) and compared the expression levels with a control set of 50 normal bone marrow (BM) samples. (Fig. 1C) Overall, these data support the PIEZO1::CBFA2T3 fusion resulted in overexpression and dysregulation of CBFA2T3 and played an essential role in leukemogenesis.
3.2 Identification of INO80C::SETBP1 fusion gene and overexpression of SETBP1
RNA-Seq identified an in-frame INO80C exon1 -SETBP1 exon3 fusion in this patient. Notably, the INO80C::SETBP1 fusion protein comprises the intact functional domains of SETBP1, suggesting the dysregulated SETBP1 function possibly contributes to oncogenesis (Fig. 1B). To confirm our speculation, we examined the patient’s expression levels of a selected list of genes (SETBP1 along with SETBP1-coexpress genes HOXA9, HOXA10, function-related genes SET, PP2A, and hematopoiesis-associated gene MECOM as well as oncogene MYB, which can be upregulated by SETBP1 and mutated SETBP1, respectively[3, 12, 13] ) with the expression levels of 50 healthy donors as a control set. Our findings indicated the aberrant upregulation of SETBP1. (Fig. 1C)
3.3 MYC and immune-related pathways are activated in this patient
RNA-Seq data analysis found the overexpression of patient-outcome-associated genes WT1, GATA2, and MYC [14–16]. Gene set enrichment analysis (GSEA) analysis was performed and the results indicated the activation of the MYC and E2F pathways, which is in concert with the upregulation of MYC. Other significantly dysregulated pathways include TGFβ, IFNγ, TNFα, and IL2_STAT5, suggesting a broad dysregulation of the immune microenvironment (Fig. 1D).