High-throughput antibody screens identify novel CML LSC-specific cell surface markers. (A) Overview of expression for 332 cell surface markers analyzed in the screen. The figure depicts the average cell surface marker expression in the Lin⁻CD34⁺CD38^−/low LSC population of 6 CML patients at diagnosis (CML Dx) relative to the expression within the same population of 3 healthy controls. Each column represents an individual marker ordered from low to high relative expression compared with the controls. (B) Identification of candidate markers that aberrantly divided the CML LSC population (ie, <10% or >90% expressed in nBM HSCs, but >10% or <90% expressed on CML LSCs). The bars represent relative expression in LSCs compared with HSCs, and the dots denote the relative expression of single patients. The red color indicates the markers that were selected for validation experiments. (C) Data from 9 markers that showed consistent aberrant expression in validation experiments using additional CML Dx samples. The plots show representative FACS data for each marker as well as pooled data (D) from 3 different CML Dx’s compared with a new healthy nBM control. Gates are set based on background expression of isotype control antibodies. The error bars show standard deviation.