To directly compare the expression levels in the two cell populations, the mean value of the signal log ratios (log2 FDC/BP3hi) was calculated for the 690 genes. The mean value of log2 FDC/BP3hi=1.4 showed that the signal intensities were 2.6-fold lower on FDC microarray (Fig. 3). It is likely that the lower signals are caused by the presence of B cells in the FDC network. This suggests that the mRNA isolated from the FDC preparations is diluted

by mRNA of co-isolated B cells causing the signal intensity to drop by nearly two-thirds. Out of the 690 genes expressed both in BP3hi stromal cells and in FDC, we defined as differentially expressed only those where the fold differences were significantly different (±1.5-fold change) from the mean value of 2.6. Using these criteria, 46.4% of the 690 genes showed equal expression in BP3hi stromal cells PI3K inhibitor and FDC (Fig. 3), supporting a close lineage relationship between FDC and BP3hi reticular cells. Genes with equal expression included BP3, used as the marker for stromal cells, and also Bgn, Mfge8 or Cxcl12. Staining of splenic tissue sections with Ab specific for the Bgn product biglycan showed that indeed its expression on the protein level is comparable. Similar staining intensities were seen for BP3hi stromal cells of the SCID mouse and for mature FDC (Fig. 4A and B). Genes which were shown to be differentially expressed in mature FDC and BPhi reticular

cells were used to dissect the complex differentiation process of reticular stromal cells. Briefly, 27.0% of the genes expressed in FDC and/or BP3hi reticular cells showed a significantly higher GSK126 nmr Carnitine palmitoyltransferase II expression in mature FDC and these included genes such as Cxcl13, Enpp2, Serpina1, Cilp, Postn, Ltbp3, Coch, Lrat and 9130213B05Rik (Fig. 3). On the other hand, 26.7% of the genes showed a significantly

higher expression in BP3hi stromal cells. These included the chemokines Ccl19 and Ccl21, which in wild-type BALB/c mice are exclusively expressed in reticular cells of the T-cell zone (Fig. 3 and Table 1). In situ hybridization confirmed for Cxcl13, Enpp2, Serpina1, Cilp, Postn, Ltbp3, Coch, Lrat and 9130213B05Rik relatively low or nondetectable expression in the reticular cells of the SCID mouse (Table 1). High expression of these genes is found only in mature FDC. On the other hand, the chemokine CXCL21 was highly expressed in reticular cells of SCID mice and, in contrast to wild-type BALB/c, equal expression was found in CXCL13+ and CXCL13− reticular cells (Fig. 4E and F). Also the gene Tmem176 showed equal expression in both subsets of reticular cells, but unlike Ccl21 no expression of Tmem176 was detectable by in situ hybridization in the spleen of wild-type BALB/c (Fig. 4E and Table 1). These findings, summarized in Table 1, show the complexity of the development of the reticular cell network which supports the lymphoid structures.