Fig 1.
Overall study design and workflow.
To identify the eQTLs associated with CML susceptibility, we performed genotyping, RNA expression profiling, in silico analysis, and functional validation using healthy individuals, CML patients, and BCR-ABL1-positive human cell line models.
Table 1.
41 SNPs selected for genotyping.
Fig 2.
RMND1 expression is correlated with the genotype of the functional SNP rs6931104 at 6q25.1.
(A) Box-plot of the significant eQTLs in both cells. RMND1 expression levels in granulocytes (left) and mononuclear cells (right) (corrected p < 0.05). (B) Manhattan plot and LD block of 6q25.1, including three significant SNPs (rs9371517, rs6931104, and rs963193). The Manhattan plot shows the p-value of the discovery set in the previous study, and the red arrows indicate these three SNPs. The LD block image was created based on the genotype information in this study.
Fig 3.
Expression of CML-susceptible gene RMND1 is affected by TF RFX3 binding affinity.
(A) The CML-associated SNP rs6931104 affects the binding affinity of transcription factor RFX3. ChIP-ed DNA enrichment determined by qRT-PCR is graphed as the amount of immunoprecipitated DNA. Error bars indicate SD values. (B) Effects of RFX3 knockdown (KD) or overexpression (OV) on RMND1 transcript levels in BCR-ABL1+ cells. Total RNA expression was assayed by RT-qPCR. Asterisk marked p-values were calculated by comparing with control in each of the three cell lines, respectively. **p < 0.01, *p < 0.05, ns–not significant. Error bars indicate SD values. (C) RMND1 transcript levels in CML patients. Total RNA expression was assayed by RT-qPCR. Minus delta Ct (GAPDH Ct value–RMND1 Ct value) indicates the expression levels (Y-axis) in samples from 12 human CML patients and 12 healthy individuals. All statistical significance was evaluated by the Student’s t-test.