More importantly, T-cell-specific genes encoding proteins such as CD3 and CD4 were absent from the FDC data sets. The comparison with the gene expression profiles

of macrophages showed an overlap in 167/575 genes. Again, the expression of genes diagnostic for macrophages such as Cd11b, Cd68 or Emr1 (F4/80) was absent or low (Signal<100) in FDC. These findings suggest that the number of follicular T cells and macrophages in the FDC network is too low to significantly distort the FDC gene expression profile. For the genes Cxcl13, Serpina1, Cilp, Lrat, Enpp2, Ltbp3, 9130213B05Rik (prostatic androgen-repressed message-1), Coch and Postn-specific expression in FDC was controlled by in situ hybridization (Fig. 2A). Staining of consecutive splenic tissue sections of BALB/c mice showed that the expression of the genes Enpp2, Serpina1, Cilp, Postn, this website Lbp3 and Lrat was restricted

to the area of CXCL13 expressing FDC. By contrast, the gene Coch showed, in addition, expression in reticular cells of the red pulp and the gene 9130213B05Rik was also expressed in reticular cells of the T-cell zone (Fig. 2A). Expression of Postn and Coch was upregulated in FDC of secondary follicles (Fig. 2B). Staining of consecutive sections with peanut agglutinin (PNA), which labels GC B cells and M2, an FDC-specific Ab, demonstrated that the upregulation of Postn and Coch is restricted to FDC in GC. The gene expression profile obtained for FDC overlapped to a large extent with that of mesenchymal cells (NCBI GEOS data base). Thus, the comparison showed that PS-341 cell line 342 of the 575 genes expressed in FDC are also expressed in myoblasts and a similar close relationship was found with the transcriptome of fibroblasts (337/575). To

analyze the lineage relationship between PRKD3 mature FDC and mesenchymal stromal cells, we made use of the fact that FDC do not develop in SCID mice. In the SCID mouse, the BP3 Ab labels reticular cells, which define the area in which lymphocyte-positive mice give rise to the B-cell compartment 19. To analyze the developmental relationship between FDC and reticular cells, BP3hi cells were micro-dissected from the spleen of SCID mice and their transcriptome examined. Since the FDC transcriptome was determined by subtraction of the B-cell signature, which includes all of the housekeeping genes (see above), we carried out the same procedure on the transcriptome of the BP3hi cells (Fig. 1A). Subtraction resulted in a set of 541 genes with significant expression in BP3hi cells. In the next step, the gene expression profile of primary FDC was compared with that of BP3hi reticular cells of the SCID mouse. This analysis yielded a set of 690 genes expressed in either one or both cell populations (Fig. 3). There was a striking similarity in the gene expression patterns of BP3hi reticular cells from SCID mice and FDC from wild-type BALB/c. In total, 85.