Disrupting the MYB–TAL1 oncogenic axis via direct intracellular delivery of synthetic zinc finger proteins

Abstract

T-cell acute lymphocytic leukemia (T-ALL) protein 1 (TAL1) is an important transcription factor in the specification of myeloid cells and positively regulates the differentiation of red blood cells. Aberrant, high-level expression of TAL1, mediated by insertions of short DNA sequences that recruit the transcription factor MYB and establish the formation of super-enhancers, causes T-ALL. Synthetic zinc finger (ZF) DNA-binding proteins targeting the MYB binding site (ZF-Myb) in Jurkat cells, a T-ALL cell line harboring the TAL1-associated mutation, bind the DNA with high affinity and efficiently outcompete MYB. Expression of ZF-Myb reduced expression of TAL1 and cell proliferation in Jurkat cells. Inclusion of a Krüppel-associated Box (KRAB) increased the ZF-Myb DNA-binding affinity four-fold and conferred more efficient reduction of TAL1 expression and Jurkat cell growth. Direct KRAB-ZF-Myb protein delivery was strongly enhanced by novel peptides (CATCH: Co-Assembling Tags based on CHarge complementarity) that form protein granules. Transcriptomic analysis revealed that downregulation of TAL1 using the synthetic KRAB-ZF-Myb protein disrupts the TAL1-MYB oncogenic axis and induces expression of pro-apoptotic genes. In summary, using a novel and highly efficient direct protein delivery system, synthetic ZF proteins targeting a single site in a super-enhancer disrupt oncogenic pathways in T-ALL.