A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells

Department of Biostatistics, Harvard School of Public Health Boston, MA, USA.
Frontiers in Genetics 10/2013; 4:209. DOI: 10.3389/fgene.2013.00209
Source: PubMed


PROM1 is the gene encoding prominin-1 or CD133, an important cell surface marker for the isolation of both normal and cancer stem cells. PROM1 transcripts initiate at a range of transcription start sites (TSS) associated with distinct tissue and cancer expression profiles. Using high resolution Cap Analysis of Gene Expression (CAGE) sequencing we characterize TSS utilization across a broad range of normal and developmental tissues. We identify a novel proximal promoter (P6) within CD133(+) melanoma cell lines and stem cells. Additional exon array sampling finds P6 to be active in populations enriched for mesenchyme, neural stem cells and within CD133(+) enriched Ewing sarcomas. The P6 promoter is enriched with respect to previously characterized PROM1 promoters for a HMGI/Y (HMGA1) family transcription factor binding site motif and exhibits different epigenetic modifications relative to the canonical promoter region of PROM1.

Download full-text


Available from: Andreas Behren
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Driven by genomic somatic variation, tumour tissues are typically heterogeneous, yet unbiased quantitative methods are rarely used to analyse heterogeneity at the protein level. Motivated by this problem, we developed automated image segmentation of images of multiple biomarkers in Ewing sarcoma to generate distributions of biomarkers between and within tumour cells. We further integrate high dimensional data with patient clinical outcomes utilising random survival forest (RSF) machine learning. Using material from cohorts of genetically diagnosed Ewing sarcoma with EWSR1 chromosomal translocations, confocal images of tissue microarrays were segmented with level sets and watershed algorithms. Each cell nucleus and cytoplasm were identified in relation to DAPI and CD99, respectively, and protein biomarkers (e.g. Ki67, pS6, Foxo3a, EGR1, MAPK) localised relative to nuclear and cytoplasmic regions of each cell in order to generate image feature distributions. The image distribution features were analysed with RSF in relation to known overall patient survival from three separate cohorts (185 informative cases). Variation in pre-analytical processing resulted in elimination of a high number of non-informative images that had poor DAPI localisation or biomarker preservation (67 cases, 36%). The distribution of image features for biomarkers in the remaining high quality material (118 cases, 104 features per case) were analysed by RSF with feature selection, and performance assessed using internal cross-validation, rather than a separate validation cohort. A prognostic classifier for Ewing sarcoma with low cross-validation error rates (0.36) was comprised of multiple features, including the Ki67 proliferative marker and a sub-population of cells with low cytoplasmic/nuclear ratio of CD99. Through elimination of bias, the evaluation of high-dimensionality biomarker distribution within cell populations of a tumour using random forest analysis in quality controlled tumour material could be achieved. Such an automated and integrated methodology has potential application in the identification of prognostic classifiers based on tumour cell heterogeneity.
    Full-text · Article · Sep 2014 · PLoS ONE
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: This chapter introduces the basic biology of CD133 (alias prominin-1), a cholesterol-binding pentaspan membrane glycoprotein that has gained enormous interest in the stem cell field. As a cell surface antigen, CD133 has become a prominent marker used for the prospective isolation and characterization of cells with stem cell properties in neural development and adult brain as well as in cancer. Beyond its application as a new biological tool for tissue engineering and regenerative therapy, CD133 has highlighted new aspects of the visual system because mutations in the PROM1 gene cause retinal pathologies. Here, we will summarize the essentials regarding the basic molecular and cellular biology of CD133 necessary for the proper evaluation of its detection in a given cell population under physiological or pathological conditions with a special focus on the neural system across species.
    Full-text · Chapter · Mar 2015