TIM-3 gene expression in leukemic stem cells vs normal HSCs. (A) Comparison of HAVCR2 (TIM-3) gene expression in CP-CML-LSC (n = 6), Accelerated phase/Blast crisis (AP/BC) LSC (n = 6) and healthy donor (HD) HSCs (n = 3) using the GSE47927 dataset. CML-LSC samples were derived from CP, AP, and BC at diagnosis and sorted based on CD34⁺CD38⁻Lin⁻CD45RA⁻CD90⁺. The HD-HSC was based on the same markers as LSC. (B) Comparison of HAVCR2 gene expression in CP-CML-LSC (n = 5) and HD-HSC (n = 5) using the GSE43754 dataset. CML-LSC samples were derived from CP at diagnosis and sorted based on CD34⁺CD38⁻ALDH high. The HD-HSC was based on the same markers as LSC. (C) Comparison of HAVCR2 gene expression in CP-CML-LSC (n = 5) and HD-HSC (n = 5) using the GSE97562 data set. CML-LSC samples were derived from CP at diagnosis and sorted based on CD34⁺CD38⁻lin⁻. The HD-HSC was based on the same markers as LSC. (D) Comparison of HAVCR2 gene expression in CP-CML-LSC (n = 18) and HD-HSC (n = 6) using the GSE76312 data set. CML-LSC samples were derived from CP at diagnosis and sorted based on Lin⁻CD34⁺CD38⁻. The HD-HSC was based on the same markers as LSC. Each dot represents average reads per kilobase of exon per million reads mapped (RPKM) from the single cells profiled for each patient. (E) The comparison of HAVCR2 gene expression of each single cells derived from 18 CP-CML-LSC single cells and 6 HD-HSC using GSE76312 data set. Total of 477 single cells in CML-LSC and 232 single cells in HD-HSC. TIM-3 expression was summarized in average RPKM for CML-LSC and HD-HSC as bar plot shown in panel F. All of the statistical analyses were performed using 2-sided unpaired t test with Welch correction.