RUNX1 C-terminal mutations impair blood cell differentiation by perturbing specific enhancer-promoter networks

Area of Science:

• Hematology
• Molecular Biology
• Cancer Genetics

Background:

• RUNX1 is crucial for blood cell formation and is often mutated in myeloid cancers.
• Mutations in the DNA-binding Runt Homology Domain (RHD) impair RUNX1 function.
• The role of RUNX1 mutations outside the RHD in disease pathogenesis remains unclear.

Purpose of the Study:

• To investigate the functional consequences of RUNX1 mutations located outside the RHD.
• To elucidate the distinct mechanisms by which these mutations contribute to hematopoietic disorders.

Main Methods:

• Analysis of patient data to identify common RUNX1 mutation sites.
• Generation of a mouse model with a specific C-terminal RUNX1 mutation (RUNX1R320*).
• Global RNA Interactions with DNA by deep sequencing (GRID-seq) to map enhancer-promoter interactions.

Main Results:

• RUNX1 mutations in the C-terminus are prevalent in hematopoietic disorders and often produce truncated proteins.
• The RUNX1R320* mutation impaired megakaryocytic differentiation via a unique transcriptional profile.
• GRID-seq revealed widespread alterations in enhancer-promoter networks and identified RUNX1R320* and FOXK2 binding at the MYC super enhancer, leading to MYC upregulation.

Conclusions:

• RUNX1 mutations outside the RHD are frequently expressed and contribute to disease through mechanisms distinct from RUNX1 loss-of-function.
• These mutant RUNX1 proteins can dysregulate hematopoiesis by altering enhancer-promoter networks and upregulating oncogenes like MYC.