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The cancer stem cell (CSC) hypothesis is an evolving oncogenesis concept. CSCs have a distinct ability to self-renew themselves and also give rise to a phenotypically diverse population of cells. Targeting CSCs represents a promising strategy for cancer treatment. Plant-derived compounds are potent in restricting the expansion of CSCs. DCLK1 has been already reported as a colon CSC specific marker. Nanoparticles can effectively inhibit multiple types of CSCs by targeting specific markers. We have synthesized DCLK1 functionalized folic acid conjugated hesperetin encapsulated chitosan nanoparticles (CFH-DCLK1), specifically to target CSCs. In this regard, we have performed proliferation assay, colony formation assay, cell migration assay, apoptosis assay, flow cytometry analysis, real-time RT- PCR and western blot analyses to determine the effect of CFH-DCLK1 and CFH nanoparticles in HCT116-colon cancer cells. In our study, we have determined the median inhibitory concentration (IC50) of CFH (47.8 µM) and CFH-DCLK1 (4.8 µM) nanoparticles in colon cancer cells. CFH-DCLK1 nanoparticles induced apoptosis and inhibited the migration and invasion of colon cancer cells. Real time PCR and western blot results have demonstrated that the treatment with CFH-DCLK1 nanoparticles significantly reduced the expression of CSC markers such as DCLK1, STAT1 and NOTCH1 compared to the CFH alone in HCT116 colon cancer cells. Finally, in the 3D spheroid model, CFH-DCLK1 nanoparticles significantly inhibited the colonosphere growth. Overall, our results highlight the effectiveness of CFH-DCLK1 nanoparticles in targeting the colon cancer cells and CSCs. This study would lead to the development of therapies targeting both cancer cells and CSCs simultaneously using nanoformulated drugs, which could bring changes in the current cancer treatment strategies. [Display omitted] • Cancer stem cells drive tumor initiation, metastasis, drug resistance and recurrence. • Nanoparticles can target cancer cells and cancer stem cells specifically. • Targeting doublecortin like kinase 1 can inhibit cancer stem cells self-renewal. • Folate receptor overexpression in cancer cells can be used for targeting therapy. [ABSTRACT FROM AUTHOR]