Lymphotoxin-β Receptor-Dependent Genes in Lymph Node and Follicular Dendritic Cell Transcriptomes

Abstract

Affinity maturation and Ab class switches occur in lymphoid germinal centers (GCs), in which differentiation and maintenance depend on lymphotoxin (LT) signaling and include differentiation of follicular dendritic cells (FDCs). The events leading to FDC and GC maturation are poorly defined. Using several approaches of functional genomics, we enumerated transcripts affected in mice by suppressing LT β receptor (LTβR) signaling and/or overrepresented in FDC-enriched GC isolates. Protein expression analysis of 3 of 12 genes both enriched in FDCs and down-regulated by LTβR signaling suppression validated them as FDC markers. Functional analysis of one of these three, clusterin, suggests a role as an FDC-derived trophic factor for GC B cells. Hence, the set of genes presented in this study includes markers emanating from LTβR signaling and transcripts relevant to GC and FDC function.

In silico subtraction approach reveals a close lineage relationship between follicular dendritic cells and BP3hi stromal cells isolated from SCID mice

“…Using highperformance chip data analysis [24], 575 genes were identified as being specifically expressed in FDC. The strongest signals in the set of FDC-specific genes were those for the chemokine Cxcl13 (Signal 5905.7) and for the apoptosis-related proteins Clu (Signal 7408.1) and Mfge8 (Signal 6220.4), all of which have been previously shown to be expressed in FDC [3,6,25].…”

“…FDC are fragile cells and are tightly associated with B cells -properties that have thus far hampered the isolation of pure FDC populations [6][7]. To overcome these problems, FDC lines have been established, however, as these cells are maintained over several weeks in culture, their phenotype no longer reflects the in vivo situation [8][9][10][11][12][13].…”

“…To overcome these problems, FDC lines have been established, however, as these cells are maintained over several weeks in culture, their phenotype no longer reflects the in vivo situation [8][9][10][11][12][13]. A number of different approaches for the enrichment and gene expression analysis of FDC have been shown to be more representative of the in vivo situation [6,8,11].…”

“…Using highperformance chip data analysis [24], 575 genes were identified as being specifically expressed in FDC. The strongest signals in the set of FDC-specific genes were those for the chemokine Cxcl13 (Signal 5905.7) and for the apoptosis-related proteins Clu (Signal 7408.1) and Mfge8 (Signal 6220.4), all of which have been previously shown to be expressed in FDC [3,6,25].To determine specific expression in FDC, the data sets were compared with those of transcriptomes from T cells, macrophages and mesenchymal cells (NCBI GEO data base). These analyses showed that only 61/575 genes expressed in cells of the FDC network are also expressed in T cells.…”

“…To overcome these problems, FDC lines have been established, however, as these cells are maintained over several weeks in culture, their phenotype no longer reflects the in vivo situation [8][9][10][11][12][13]. A number of different approaches for the enrichment and gene expression analysis of FDC have been shown to be more representative of the in vivo situation [6,8,11].From a number of experiments, it is apparent that FDC are a highly specialized subset of reticular cells [14][15][16][17][18]. Using BP3, an ectoenzyme of the NAD glycohydrolase family, as a marker antigen for the splenic reticular network of stromal cells, one can distinguish the reticulum cells in the B-cell area from those in the T-cell zone.…”