Evaluation of PTBP1 binding at transcripts in the human acute myeloid leukemia cell line MOLM-13

To systematically evaluate their necessity in cancer, we performed domain-focused CRISPR screens targeting RNAes and RBPs across a broad spectrum of cancer cell lines. These screens identified novel acute myeloid leukemia (AML) dependencies, including PTBP1, with a bias toward KMT2A-rearranged (KMT2A-r) AML, an aggressive subtype with poor clinical outcomes.

Genetic and cellular validation confirmed all four RNA-binding domains in PTBP1 are required for KMT2A-r AML proliferation. PTBP1 loss led to cell cycle arrest, apoptosis, and induction of myeloid differentiation programs. Transcriptomic analyses revealed widespread dysregulation of gene expression and splicing. eCLIP-seq further showed PTBP1 binds to a subset of these transcripts critical for AML proliferation, including ACSL4, DPF2, and IKZF1.