Human cord blood (CB)-derived CD133؉ cells carry characteristics of primitive hematopoietic cells and proffer an alternative for CD34 ؉ cells in hematopoietic stem cell (HSC) transplantation. To characterize the CD133 ؉ cell population on a genetic level, a global expression analysis of CD133 ؉ cells was performed using oligonucleotide microarrays. CD133؉ cells were purified from four fresh CB units by immunomagnetic selection. All four CD133؉ samples showed significant similarity in their gene expression pattern, whereas they differed clearly from the CD133 ؊ control samples. In all, 690 transcripts were differentially expressed between CD133؉ and CD133 ؊ cells. Of these, 393 were increased and 297 were decreased in CD133 ؉ cells. The highest overexpression was noted in genes associated with metabolism, cellular physiological processes, cell communication, and development. A set of 257 transcripts expressed solely in the CD133 ؉ cell population was identified. Colonyforming unit (CFU) assay was used to detect the clonal progeny of precursors present in the studied cell populations. The results demonstrate that CD133؉ cells express primitive markers and possess clonogenic progenitor capacity. This study provides a gene expression profile for human CD133 ؉ cells. It presents a set of genes that may be used to unravel the properties of the CD133 ؉ cell population, assumed to be highly enriched in HSCs. STEM CELLS 2006;24: 631-641

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CD34 and CD133 are the most commonly used markers to enrich hematopoietic stem cells (HSCs). Positively selected HSCs are increasingly used for autologous and allogeneic transplantation, yet the biological properties of CD34(+) and CD133(+) cells are largely unknown. In the present study, a genome-wide gene expression analysis of human cord blood (CB)-derived CD34(+) cells was performed. The CD34(+) gene expression profile was compared to an identically constructed CD133(+) gene expression profile to reveal the specific expression patterns and major differences of CD34(+) and CD133(+) cells. As expected, many genes were similarly expressed in the two cell populations, but cell-type-specific gene expression was also demonstrated. Self-organizing map analysis was used to identify transcripts having similar expression patterns, and the results were compared between CD34(+) and CD133(+) cells. Also, a prioritization algorithm was used to rank the genes best separating CD34(+) and CD133(+) cells from their CD34() and CD133() counterparts in CB. Our results show that CD133(+) cells have higher numbers of up-regulated genes than CD34(+) cells. Furthermore, the uniquely expressed genes in CD34(+) or CD133(+) cell populations were associated with different biological processes. CD34(+) cells overexpressed many transcripts associated with development and response to stress or external stimuli. In CD133(+) cells, the most significantly represented biological processes were establishment and maintenance of chromatin architecture, DNA metabolism, and cell cycle. The differences between the gene expression profiles of CD34(+) and CD133(+) cells indicate the more primitive nature of CD133(+) cells. These profiles suggest that CD34(+) and CD133(+) cells may have different roles in hematopoietic regeneration.