Cancer stem cells – CD133+ and chromosome 19 deletions


Cancer stem cells (CSCs) represent an extremely small subpopulation of tumor cells and are characterized by the ability to self-renew and differentiate. This special group of tumor cells has a slower growth rate relative to other tumor cells, endowing CSCs with high resistance to traditional chemo and radiation therapies that target rapidly dividing cells (1). Because of their resistance to treatment, research into understanding the molecular basis of CSC stemness has been highly pursued.

Several cell surface markers have been identified for CSCs; these include CD34 (Cluster of Differentiation 34), CD133 (Prominim 1) and CD44. These proteins are one of the criteria used for defining a tumor cell as a CSC, and have enabled the development of immuno-capture methodologies for CSC enrichment from larger tumor cell populations for study (1). More recently, additional functional markers associated with intrinsic stem properties, such as PI3Kα, AKT-2 and TWIST1, have been applied to the immune-capture approach for CSCs and commercial kits using this strategy are available, for example, the AdnaTest EMT-2 CancerSelect Kit.

CD133 (Prominim 1) has been identified in CSCs from glioblastoma, prostate, colon, lung, pancreatic and ovarian cancers, as well as melanoma (1). CD133 is a 120 kDa transmembrane protein (comprising of 865 amino acids) encoded by a single-copy gene on chromosome 4 (4p15.33) in humans, and chromosome 5(5b3) in mice. Its tertiary protein structure consists of an N-terminal extracellular domain, five transmembrane domains with two large extracellular loops and a 59 amino acid cytoplasmic tail. In addition to CD133 serving as a biomarker for CSCs, it has also been demonstrated to participate in cell growth, development and tumor biology (2). CD133 gene expression appears to be regulated by many extracellular and intracellular factors. Factors associated with CD133 upregulation in cells (termed CD133+ cells) include hypoxia, inhibition of mTOR activity, TGFβ, Toll-like receptors [TR7 & 8], miR-130b and CD133 demethylation (2).

A recent study by Cervantes-Madrid et al. (2017) examined the genomics of CSCs, specifically of colorectal CSCs. In particular, the study focused on defining genomic alterations found in CD133+ vs CD133-/EpCAM+ cells (3). Fresh interoperative human tumor biopsies from 27 colorectal cancer study participants were used to enrich for CD133+ and CD133-/EpCAM+ cells by immunomagnetic separation. DNA and RNA were isolated from cell fractions using the AllPrep DNA/RNA Micro Kit.  CD133 expression levels were compared for the two cell types using the QuantiTect Reverse Transcription Kit and qPCR. Results confirmed PROM1 ( = CD133 gene) plus a second cancer stem cell gene (GMP7) had increased expression levels in CD133+ cells compared to CD133-/EpCAM+ cells. Following whole genome amplification (WGA) of single cells using the REPLI-g Single Cell Kit, array comparative genome hybridization (aCGH) was performed against the WGA reference DNA. DNA alterations in the two cell fractions showed great heterogeneity. Overall, aCGH results indicated that deletions corresponded to 87% of DNA alterations in all samples, and were more common than amplifications. Deletions detected in both CD133+ and CD133-/EpCAM+, and which were also found in >50% of participants, were located on chromosomes 1,2,7,8,10,12,14,15,16,18 and 19. Deletion of chromosome 19p occurred in 27 samples representing 18 patients. Additionally, qPCR assays, performed at four regions of chromosome 19p to see if these deletions were also detected in corresponding tumor tissue, only detected deletions in 6 of 20 participants at the tumor tissue level. Because chromosome 19 is an extremely dense chromosome with respect to genes, a deletion of the p-arm affects multiple genes. Thus, an important change for tumor progression may be the observed deletion of chromosome 19p, which was detected in both CD133+ and CD133-/EpCAM+ cell fractions in the majority of these participants, and involves 575 genes and miRNAs.

Interested in a solution for the enrichment of cancer stem cells? Check out our AdnaTest EMT-2/StemCell CancerSelect Kit and see what it can do for your research. If you’re looking to generate high-diversity whole genome libraries from single cells, then have a look at our QIAseq FX Single Cell DNA Library Kit.



  1. 1. Chen W, et al. (2016) Cancer stem cell quiescence and plasticity as major challenges in cancer therapy. Stem Cells Int. 2016.  2016:1740936. doi:10.1155/2016/1740936. [Link]
  2. 2. Li, Z. (2013) CD133: a stem cell biomarker and beyond. Exp Hematology & Oncology 2:17. [Link]
  3. 3. Cervantes-Madrid,D. et al. (2017) DNA alterations in CD133+ and CD133- tumour cells enriched from intra-operative human colon tumour biopsies.  BMC Cancer 17:219. [Link]
Joby Chesnick

Dr. Joby Chesnick is a Senior Global Marketing Manager in Demand Generation at QIAGEN. She received her Ph.D. in Biology, with doctoral research specializing in unicellular algal symbioses at Texas A&M University. Afterwards, she was awarded an NSF Post-Doctoral Fellowship in Plant Biology and investigated organelle acquisition by primitive eukaryotes at the University of Washington in Seattle. In 2007, Joby additionally received her M.B.A. from the University of Wisconsin-Madison. Her work experience spans 18 years in the biotech industry, and includes positions in bioinformatics support, technical support, intellectual property, product management, and sales prior to joining QIAGEN in January 2017.

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