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Indian gooseberry, also known as amla, a widely consumed fruit in South Asia, was evaluated for its anti-proliferative and pro-apoptotic mechanisms on human colon cancer stem cells (HCCSC). Amla extracts suppressed proliferation and induced apoptosis independent of p53, a tumour suppressor gene, in HCCSCs. Further, amla extracts suppressed cell proliferation by targeting the Wnt/β-catenin signalling pathway as seen by decreased nuclear translocation of β-catenin. Additionally, this led to suppressed expression of c-Myc and cyclin D1, key proteins involved in cell proliferation. Inhibition of stem-ness of HCCSCs by amla may be due to its effect on the Wnt/β-catenin signalling. These results indicate that amla suppresses HCCSC proliferation and induces apoptosis independent of p53 status via potentially targeting Wnt/β-catenin signalling pathway. Amla is therefore a promising functional food for preventing colon cancer and might be a novel resource for the food industry.