Alkaline phosphatase (ALP) is known to be a marker for several somatic stem cells and cancer cells. We found that human squamous cell carcinoma HeLa cells are comprised by ALP-positive and negative cells. Single cell-derived colony assay revealed that the former cells are labile with respect to ALP activity, but the latter are stable. We cloned ALP-negative cells from the HeLa cells, and named H-1 clone. DNA microarray analysis revealed that gene expression pattern of H-1 cells is almost the same with that of their parental HeLa cells, but several genes for glycoprotein hormone alpha chain, ras-related and estrogen-regulated growth inhibitor, ALP, and Frizzled-10 was respectively 18.2, 9.6, 9.2 and 10.5–fold are upregulated in the HeLa cells. Although there is no evidence that the ALP-positive cells are cancer stem cells (CSCs) at present, HeLa cells comprised by ALP-positive and -negative cells may be a good model for CSC study in future. HeLa cells consist of two cell types, namely alkaline phosphatase (ALP)-positive and negative cells. To distinguish gene expression pattern between these two types of cells, microarray analysis was performed using HeLa cells (parental cell line; a mixture of ALP-positive and negative cells) and H-1 cells, ALP-negative cells derived from HeLa cells
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