Allelic expression imbalance of CDKN2A variants in childhood acute lymphoblastic leukemia

Germline CDKN2A variant predisposes to childhood acute lymphoblastic leukemia (ALL) through allelic expression imbalance (AEI). It is unknown, therefore, how these germline variations work and whether they all confer B-ALL susceptibility through AEI.

Using allele-specific Taqman PCR assays, we demonstrated that preferentially expressed of those functional inherited coding variants in leukemic cells compared to hematopoietic cells. In an inherent p 16^Ink4a-defective Ba/F3 cell model overexpressing functional p16^INK4A variants showed enhanced susceptibility to transformation by BCR-ABL1-, NRAS^G12D-, and JAK2^R683G + CRLF2-. Notably, the variant p16^INK4A exhibited higher transcription level than wild-type allele in co-expression studies. While CDK4/6 inhibitor partially suppressed NRAS^G12D-, and JAK2^R683G + CRLF2-induced transformation, it proved ineffective against BCR-ABL1-induced leukemic transformation. Differential gene expression analysis revealed upregulation of m6A-related gene PRRC2A, whose knockout partially restored wild-type p16^INK4A expression.

These findings illuminate how inherited CDKN2A genetic variations of coding region influence ALL development through AEI mechanisms.