Differential RUNX1-Isoform Specific Autoregulation of RUNX1 and Regulation of Target Genes (PCTP, MYL9) in Megakaryocytic Cells

RUNX1 is an essential transcription factor for hematopoiesis. Human germline RUNX1 haplodeficiency is associated with impaired megakaryocyte differentiation, thrombocytopenia, platelet dysfunction and predisposition to myeloid malignancies. The two major RUNX1 isoforms RUNX1C and RUNX1B differ at N-terminus by 14AA, and are regulated by two distinct promoters P1 and P2, respectively. RUNX1B and RUNX1C have distinct roles and tissue expression. Little is known regarding the differential effects of RUNX1 isoforms in RUNX1 autoregulation, and on their regulation of target genes. There are 5 RUNX1 consensus binding sites located in P1 promoter and one RUNX1 site in P2 promoter. To study RUNX1 promoters, both WT RUNX1 P1 and P2 promoter regions were individually cloned into PGL4 luciferase promoter vector. ChIP studies using PMA-treated megakaryocytic HEL cells showed RUNX1 binding to chromatin regions encompassing the RUNX1 binding sites in both promoters. Mutations of 2 RUNX1 binding sites in intron region of P1 promoter reduced promoter activity; mutations of first 2 RUNX1 binding sites in at the exon region of P1 promoter increased activity. Mutation of single RUNX1 binding site in P2 promoter increased promoter activity. Thus, RUNX1 binds to P1 and P2 promoters to regulate their activities. To examine the RUNX1 autoregulation by individual isoforms, we co-transfected each isoform with P1 or P2 promoter vector in HeLa cells, which express negligible endogenous RUNX1. In response to RUNX1B, P1 promoter showed a dose-dependent decrease in promoter activity. RUNX1C expression, increased P1 promoter activity in a dose-dependent manner. With constant RUNX1C expression, increase in RUNX1B co-expression led to a dose-dependent decrease in P1 promoter activity. In HeLa cells RUNX1B decreased P2 promoter activity in a dose-dependent manner. With constant RUNX1B expression, an increase in RUNX1C increased RUNX1 P2 promoter activity. Thus, RUNX1B and RUNX1C regulate both P1 and P2 promoters in a distinct manner. In studies in megakaryocytic HEL cells, which express endogenous RUNX1, RUNX1B overexpression decreased RUNX1C expression by 50%. RUNX1C overexpression increased by 2-fold RUNX1B protein. In studies using RUNX1C-specific antibody, and expression plasmids for hemagglutinin-tagged-RUNX1B and c-Myc-tagged RUNX1C, RUNX1B overexpression decreased RUNX1C; RUNX1C overexpression increased RUNX1B. These studies indicate that RUNX1 isoforms autoregulate in a differential manner at the protein level. We studied the effects of RUNX1 isoforms on two established downstream RUNX1 target genes PCTP (phosphatidylcholine transfer protein) and MYL9(myosin light chain) in HeLa cells. RUNX1B overexpression increased both PCTP and MYL9 protein on immunoblotting, while RUNX1C overexpression reduced both proteins. This suggests RUNX1B and RUNX1C have differential effects in regulating downstream genes. These findings are in line with our studies in whole blood from a large cohort of patients with CAD showing a positive correlation between PCTP (Circulation 2017136(10):927-939) with RUNX1B transcript levels and a negative relationship with those for RUNX1C. Conclusions: RUNX1 isoforms autoregulate RUNX1 expression differentially in an isoform-specific manner. Moreover, they regulate target genes (MYL9 and PCTP) in a differential manner. These RUNX1 isoform-specific effects may be important in understanding the consequences of germline RUNX1 haplodeficiency and in modulating RUNX1 levels for therapeutic purposes.