title: The CDX1-microRNA-215 axis regulates colorectal cancer stem cell differentiation.
abstract: The transcription factor caudal-type homeobox 1 (CDX1) is a key regulator of differentiation in the normal colon and in colorectal cancer (CRC). CDX1 activates the expression of enterocyte genes, but it is not clear how the concomitant silencing of stem cell genes is achieved. MicroRNAs (miRNAs) are important mediators of gene repression and have been implicated in tumor suppression and carcinogenesis, but the roles of miRNAs in differentiation, particularly in CRC, remain poorly understood. Here, we identified microRNA-215 (miR-215) as a direct transcriptional target of CDX1 by using high-throughput small RNA sequencing to profile miRNA expression in two pairs of CRC cell lines: CDX1-low HCT116 and HCT116 with stable CDX1 overexpression, and CDX1-high LS174T and LS174T with stable CDX1 knockdown. Validation of candidate miRNAs identified by RNA-seq in a larger cell-line panel revealed miR-215 to be most significantly correlated with CDX1 expression. Quantitative ChIP-PCR and promoter luciferase assays confirmed that CDX1 directly activates miR-215 transcription. miR-215 expression is depleted in FACS-enriched cancer stem cells compared with unsorted samples. Overexpression of miR-215 in poorly differentiated cell lines causes a decrease in clonogenicity, whereas miR-215 knockdown increases clonogenicity and impairs differentiation in CDX1-high cell lines. We identified the genome-wide targets of miR-215 and found that miR-215 mediates the repression of cell cycle and stemness genes downstream of CDX1. In particular, the miR-215 target gene BMI1 has been shown to promote stemness and self-renewal and to vary inversely with CDX1. Our work situates miR-215 as a link between CDX1 expression and BMI1 repression that governs differentiation in CRC.
authors.affiliation: Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom; and Regulatory RNAs and Cancer Section and.
authors.forename: Matthew F
authors.initials: MF
authors.lastname: Jones
authors.affiliation: Regulatory RNAs and Cancer Section and.
authors.forename: Toshifumi
authors.initials: T
authors.lastname: Hara
authors.affiliation: Molecular Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.
authors.forename: Princy
authors.initials: P
authors.lastname: Francis
authors.affiliation: Regulatory RNAs and Cancer Section and.
authors.forename: Xiao Ling
authors.initials: XL
authors.lastname: Li
authors.affiliation: Molecular Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.
authors.forename: Sven
authors.initials: S
authors.lastname: Bilke
authors.affiliation: Molecular Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.
authors.forename: Yuelin
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Molecular Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.
authors.forename: Marbin
authors.initials: M
authors.lastname: Pineda
authors.affiliation: Regulatory RNAs and Cancer Section and.
authors.forename: Murugan
authors.initials: M
authors.lastname: Subramanian
authors.affiliation: Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom; and walter.bodmer@hertford.ox.ac.uk ashish.lal@nih.gov.
authors.forename: Walter F
authors.initials: WF
authors.lastname: Bodmer
authors.affiliation: Regulatory RNAs and Cancer Section and walter.bodmer@hertford.ox.ac.uk ashish.lal@nih.gov.
authors.forename: Ashish
authors.initials: A
authors.lastname: Lal
mesh_terms: D002454:Cell Differentiation; D045744:Cell Line, Tumor; D003106:Colon / Q000378:metabolism; D015179:Colorectal Neoplasms / Q000378:metabolism*; D018899:CpG Islands; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D045325:HCT116 Cells; D018398:Homeodomain Proteins / Q000378:metabolism*; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D014411:Neoplastic Stem Cells / Q000166:cytology*; D063150:Polycomb Repressive Complex 1 / Q000378:metabolism; D017423:Sequence Analysis, RNA; D014162:Transfection
chemical_list: C069077:BMI1 protein, human; C491273:CDX1 protein, human; D018398:Homeodomain Proteins; C553667:MIRN215 microRNA, human; D035683:MicroRNAs; D063150:Polycomb Repressive Complex 1
keywords: CDX1; cancer stem cells; colorectal cancer; miR-215; miRNA