Rat umbilical cord matrix stem cells (UCMSC) have been shown to exhibit a remarkable ability to control rat mammary adenocarcinoma (Mat B III) cell proliferation both in vivo and in vitro. To study the underlying mechanisms and genes involved in Mat B III growth attenuation, total RNA was extracted from the naive rat UCMSC alone and those cocultured with Mat B III in Transwell culture dishes. Gene expression profiles of naive rat UCMSC alone and those cocultured with Mat B III cells were investigated by microarray analysis using an Illumina RatRef-12 Expression BeadChip. The comparison of gene expression profiles between untreated and cocultured rat UCMSC identified five upregulated candidate genes (follistatin (FST), sulfatase1 (SULF-1), glucose phosphate isomerase (GPI), HtrA serine peptidase (HTRA1), and adipocyte differentiation-related protein (ADRP)) and two downregulated candidate genes (transforming growth factor, beta-induced, 68 kDa (TGFβI) and podoplanin (PDPN)) based upon the following screening criteria: (1) expression of the candidate genes should show at least a 1.5-fold change in rat UCMSC cocultured with Mat B III cells; (2) candidate genes encode secretory proteins; and (3) they encode cell growth-related proteins. Following confirmation of gene expression by real-time PCR, ADRP, SULF-1 and GPI were selected for further analysis. Addition of specific neutralizing antibodies against these three gene products or addition of gene-specific siRNA's individually in cocultures of 1:20 rat UCMSC:Mat B III cells significantly increased cell proliferation, implying that these gene products are produced under the cocultured condition and functionally attenuate cell growth. Immunoprecipitation followed by Western blot analysis demonstrated that these proteins are indeed secreted into the culture medium. Individual overexpression of these three genes in rat UCMSC significantly enhanced UCMSC-dependent inhibition of cell proliferation in coculture. These results suggest that ADRP, SULF-1 and GPI act as tumor suppressor genes, and these genes might be involved in rat UCMSC-dependent growth attenuation of rat mammary tumors.