The Role of RUNX1 Gene Expression Variation in Down Syndrome-Related Leukemia. K.J. Duffy, M. Olivier. Physiology, Medical College of Wisconsin, Milwaukee, WI.
   Trisomy 21, the cause of Down syndrome, affects 1 in every 800 to 1000 live births today. The phenotypes associated with this chromosomal abnormality range in severity and include an increased risk for several types of leukemia. Because children with trisomy 21 have a 20 times greater chance of developing acute myeloid leukemia and a 500 times greater chance of developing acute megakaryoblastic leukemia (AMKL), it is reasonable to postulate that the over-expression of genes on chromosome 21 may play a critical role in this process. RUNX1, a gene located on chromosome 21, plays a crucial role in the development of other acute myeloid leukemia (AML) subtypes. Here, we examined the linkage disequilibrium structure of the RUNX1 gene region and analyzed whether individual common haplotypes lead to over-expression of RUNX1, an effect that would be further potentiated in trisomy 21. Using the HapMap CEPH genotype data, we identified 95 blocks of high linkage disequilibrium (LD) across a 2Mb region of interest. We determined the common haplotypes (frequency >5%) in each of the eight largest LD blocks, the average size being 30kb. We subsequently identified CEPH individuals homozygous for common haplotypes within each block. Using lymphoblastoid cell lines (Coriell Cell Repository) for these homozygous individuals, we measured the relative mRNA expression levels of RUNX1 by real-time PCR. One of the eight blocks of LD showed a significant difference in RUNX1 mRNA expression between haplotypes. The block is 35kb in size and located in the middle of the RUNX1 gene. Six tag SNPs define seven common haplotypes in this block. Of these, cell lines homozygous for haplotype 2 (frequency 30%) showed significantly increased RUNX1 mRNA expression versus all other haplotypes tested. Expression was elevated approximately 1.7 fold (p<.0002). This haplotype-specific difference in RUNX1 gene expression in chromosomally normal cell lines suggests that sequence variants within RUNX1 combined with an over-expression of RUNX1 in trisomy 21 may play a functional role in the development of trisomy 21-related AMKL.