Gene expression profile of mesenchymal stem cells from paired umbilical cord units: cord is different from blood

Abstract

Mesenchymal stem cells (MSC) are multipotent cells which can be obtained from several adult and fetal tissues including human umbilical cord units. We have recently shown that umbilical cord tissue (UC) is richer in MSC than umbilical cord blood (UCB) but their origin and characteristics in blood as compared to the cord remains unknown. Here we compared, for the first time, the exonic protein-coding and intronic noncoding RNA (ncRNA) expression profiles of MSC from match-paired UC and UCB samples, harvested from the same donors, processed simultaneously and under the same culture conditions. The patterns of intronic ncRNA expression in MSC from UC and UCB paired units were highly similar, indicative of their common donor origin. The respective exonic protein-coding transcript expression profiles, however, were significantly different. Hierarchical clustering based on protein-coding expression similarities grouped MSC according to their tissue location rather than original donor. Genes related to systems development, osteogenesis and immune system were expressed at higher levels in UCB, whereas genes related to cell adhesion, morphogenesis, secretion, angiogenesis and neurogenesis were more expressed in UC cells. These molecular differences verified in tissue-specific MSC gene expression may reflect functional activities influenced by distinct niches and should be considered when developing clinical protocols involving MSC from different sources. In addition, these findings reinforce our previous suggestion on the importance of banking the whole umbilical cord unit for research or future therapeutic use.

Fig. 1

Characterization of adherent cells isolated from UCB and UC. a, c Flow cytometric analysis of cell surface markers of MSC from UCB and UC, respectively. Representative histograms are demonstrated, and their respective controls are shown by the black lines. b, d Morphology of adherent cells isolated from UCB and UC. After 15 days in culture, all isolated MSC populations displayed a spindle-shaped morphology. e Differentiation potential of adherent cells isolated from UCB and UC. Osteogenic differentiation of adherent cells from UCB and UC was demonstrated by calcium deposition shown by von Kossa stain; Adipogenesis was detected by the formation of intracytoplasmic lipid droplets stained with oil red O; Cell spheres from UCB and UC were stained with toluidine blue to confirm chondrogenic differentiation. Mucopolysaccharide-rich extracellular matrix is shown in pinkish metachromatic areas. Abbreviations: CD cluster of differentiation; HLA-ABC human leukocyte antigen-ABC; HLA-DR human leukocyte antigen-DR; UCB umbilical cord blood; UC umbilical cord

Fig. 2

Non-supervised hierarchical clustering of a all 10,935 protein-coding genes and b all 7,170 intronic noncoding RNAs, expressed in MSC from UC and UCB. Each row represents the relative levels of expression for a single gene, calculated as the number of standard deviations above (red) or below (green) the mean expression level of that gene across the samples. Each column represents the average expression of two technical replicate (Cy3 and Cy5) measurements of each sample. In a MSC isolated from the same tissue clustered together while MSC from different tissues (UC or UCB) and same donors are found in different clusters. In b MSC isolated from different tissues (UC or UCB) and the same donor clustered together while MSC from the same tissue and different donors are found in different clusters

Fig. 3

Expression signature of protein-coding transcripts in MSC from UC and UCB. A total of 1,870 genes with significantly different levels among MSC from UC and UCB samples were identified by SAM one-class statistical analysis (FDR < 5%) and hierarchically clustered as described in Materials and Methods. Each row represents the relative levels of expression for a single gene, calculated as the number of standard deviations above (red) or below (green) the average expression level of that gene across the samples. Each column represents the average expression of two technical replicate (Cy3 and Cy5) measurements of each sample