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Effect on gene expression and RNA splicing with CRISPR/Cas9 knockout of PTBP1, PTBP2, or both in MOLM-13, MV4-11, and K-562 human leukemia cell lines

ABSTRACT: RNA-modifying enzymes (RNAes) and RNA-binding proteins (RBPs) have emerged as critical gene regulators in both normal physiology and cancer. 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. Our findings demonstrate that PTBP1 supports AML proliferation by fine-tuning the expression and splicing of AML-essential genes and provide a workflow for systematically annotating RNAe and RBP dependencies in cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE306536 | GEO | 2026/08/10

REPOSITORIES: GEO

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