Abstract Curcumin induces apoptotic/autophagic cell death of colon cancer cells, and targets cancer stem cells (CSC). In here, we examined for the first time, possible apoptotic/autophagic effects of curcumin on colon CSCs, positive for DCLK1/CD44/LGR5. Curcumin (20-25µM) caused significant loss in the expression of stem cell markers DCLK1/CD44/ALDHA1/LGR5, along with down-regulation of several pluripotency factors, in tumorspheres and xenografts derived from human colon cancer cells. Surprisingly, curcumin induced proliferation and autophagic survival of a small subset of DCLK1+ve CSCs. Colon cancer tumorspheres were disintegrated by curcumin, but regrew as secondary tumorspheres after 30-40 days, suggesting the novel possibility that autophagy-associated survival may allow CSCs to survive and regrow as tumorspheres. We next examined inhibitory effects of DCLK1-siRNA. Unlike curcumin, DCLK1-siRNA only induced apoptotic cell death, with no autophagic response. Combination of curcumin+DCLK1-siRNA caused massive apoptotic/autophagic cell death of colon cancer cells growing as tumorpsheres or xenografts, and reversed the transformed phenotype of CSCs, as previously reported by us (Int.J.Cancer, 2012). Co-treatment with curcumin+DCLK-siRNA was more effective that either agent alone in: 1)attenuating growth of tumorspheres, 2)shrinking the pre-formed xenografts in vivo, and 3)eliminating relapse (re-growth) of tumorspheres. We recently discovered that colon cancer cells and adenocarcinomas from patients express DCLK1-short (S) isoform , transcribed from intron-V promoter; long (L) isoform was silenced by promoter methylation. Normal intestinal cells and non-transformed epithelial cells, on the other hand, mainly expressed DCLK1-L isoform. Promoter-reporter studies and ChIP assays demonstrated that curcumin significantly reduced expression levels of DCLK1-S isoform in colon cancer cells but paradoxically increased its expression in non-transformed/normal intestinal cells. Thus, the differential effects of curcumin on DCLK1 expression in cancer vs normal cells may explain the underlying mechanisms by which curcumin targets CSCs while sparing normal stem cells. Conclusion. Our studies strongly suggest that, 1) DCLK1 represents a functional protein for colon cancers, 2) combination of curcumin+DCLK1-siRNA may target and eradicate colon cancer stem cells., and 3) identifying small molecules that inhibit expression of S-isoform may allow to specifically target cancer stem cells, while sparing normal stem cells for cancer treatment purposes. This work was supported by NIH Granst to PS (R01CA09795909 and RO1CA0975909-S1). Citation Format: Shubhashish Sarkar, Malaney O'Connell, Carla, Kantara, Pomila Singh. A sub-set of DCLK1+ve colon cancer stem cells (CSCs) survive curcumin induced autophagy, while co-treatment with curcumin +DCLK1-siRNA eliminates CSCs: Role of long and short isofoms of DCLK1. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3903. doi:10.1158/1538-7445.AM2014-3903