The Splicing Factor PTBP1 interacts with RUNX1 and is Required for Leukemia Cell Survival

Dhir, A.; Ethell, A.; Watkins, R.; Lam, C.; Tur-Rodriguez, K.; Persinger, J.; Dobish, K. K.; Panda, S.; Buckley, S. M.; Swenson, S. A.; Brahma, S.; Rowley, M. J.; Hyde, R. K.

doi:10.1101/2025.05.16.654547

bioRxiv · 10.1101/2025.05.16.654547

The Splicing Factor PTBP1 interacts with RUNX1 and is Required for Leukemia Cell Survival

Dhir, A.·Ethell, A.·Watkins, R.·Lam, C.·Tur-Rodriguez, K.·Persinger, J.·Dobish, K. K.·Panda, S.·Buckley, S. M.·Swenson, S. A.·Brahma, S.·Rowley, M. J.·Hyde, R. K.

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Abstract

Runt-related Transcription Factor 1 (RUNX1) is essential for definitive hematopoiesis and is among the most frequently mutated genes in leukemia. Previous work from our lab demonstrated that Histone Deacetylase 1 (HDAC1), a known RUNX1 partner, is unexpectedly required for active transcription suggesting a non-histone role for HDAC1 regulating components of the RUNX1 complex. Here, we use proteomics, genomics, and long-read transcriptomics to identify novel RUNX1 interacting partners and decipher their role in gene regulation and RNA splicing in leukemia cells. We demonstrate that Polypyrimidine Tract Binding Protein 1 (PTBP1) interacts with RUNX1 in an HDAC1 dependent manner. Chromatin profiling revealed extensive genome-wide overlap in sites occupied by RUNX1 and PTBP1, with significant enrichment at promoters of actively transcribed genes. Loss of PTBP1 in AML cells led to widespread alterations in RNA splicing and decreased expression of genes whose promoters are bound by both factors, including metabolic genes. In agreement with these findings, we found that loss of PTBP1 reduced glycolysis and glucose uptake and ultimately caused cell death. Based on our data, we propose that the interaction between RUNX1 and PTBP1 facilitates expression of metabolic proteins essential for leukemia cell growth and survival. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/654547v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@74e3b9org.highwire.dtl.DTLVardef@12a090org.highwire.dtl.DTLVardef@eb5a48org.highwire.dtl.DTLVardef@17465dc_HPS_FORMAT_FIGEXP M_FIG C_FIG KEY POINTSO_LIPTBP1 binds RUNX1 in a HDAC1-dependent manner and co-localizes to the promoters of target genes in leukemia cells. C_LIO_LILoss of PTBP1 decreases expression of key metabolic genes, resulting in decreased cell growth and glycolysis, increased sensitivity to chemotherapy, and cell death. C_LI

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Dhir, A., Ethell, A., Watkins, R., Lam, C., Tur-Rodriguez, K., Persinger, J., Dobish, K. K., Panda, S., Buckley, S. M., Swenson, S. A., Brahma, S., Rowley, M. J., Hyde, R. K.. 2025-05-21. The Splicing Factor PTBP1 interacts with RUNX1 and is Required for Leukemia Cell Survival. https://doi.org/10.1101/2025.05.16.654547

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