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Purpose: To investigate whether carbon ion irradiation had beneficial effects by targeting cancer stem cells, human glioma stem cells were treated by carbon ion or X-rays irradiation.Materials and methods: CD133-expressing tumour cells were isolated by MACS in human glioma cells line M059K and M059J; CD1331 fractions were assayed by FACS after IR treatment; Colony formation and soft agar assayed survival and proliferation; Western analysis the DNA damage checkpoint response.Results: The fraction of tumour cells expressing CD133, a marker for both neural stem cells and brain cancer stem cells is enriched after radiation in gliomas.In both cell culture and the colonies formed in soft agar, CD133-positive tumour cells represent the cellular population that confers glioma radioresistance, whether heavy ion or X-rays.The relative biological effectiveness (RBE) value of carbon ion relative to X-rays was calculated to be 1.99 in CD133-expressing tumour cells (D10 survival fraction) and 1.71 in CD133-negative tumour cells.CD133-expressing tumour cells preferentially activate the DNA damage checkpoint in response to radiation, and repair radiation-induced DNA damage more effectively than CD 133-negative tumour cells.Conclusions: Our results suggest that CD133-positive tumour cells represent the cellular population that confers glioma radioresistance and could be the source of tumour recurrence after radiation.But heavy ion irradiation has a great potential to effectively target radioresistant cancer stem cells.This is considered to be one of the major contributing factors for the high radiocurability of heavy ion cancer treatment.