Identification of co-expressed gene signatures in mouse B1, marginal zone and B2 B-cell populations - PubMed (original) (raw)

Identification of co-expressed gene signatures in mouse B1, marginal zone and B2 B-cell populations

Neil A Mabbott et al. Immunology. 2014 Jan.

Abstract

In mice, three major B-cell subsets have been identified with distinct functionalities: B1 B cells, marginal zone B cells and follicular B2 B cells. Here, we used the growing body of publicly available transcriptomics data to create an expression atlas of 84 gene expression microarray data sets of distinct mouse B-cell subsets. These data were subjected to network-based cluster analysis using BioLayout Express(3D). Using this analysis tool, genes with related functions clustered together in discrete regions of the network graph and enabled the identification of transcriptional networks that underpinned the functional activity of distinct cell populations. Some gene clusters were expressed highly by most of the cell populations included in this analysis (such as those with activity related to house-keeping functions). Others contained genes with expression patterns specific to distinct B-cell subsets. While these clusters contained many genes typically associated with the activity of the cells they were specifically expressed in, many novel B-cell-subset-specific candidate genes were identified. A large number of uncharacterized genes were also represented in these B-cell lineage-specific clusters. Further analysis of the activities of these uncharacterized candidate genes will lead to the identification of novel B-cell lineage-specific transcription factors and regulators of B-cell function. We also analysed 36 microarray data sets from distinct human B-cell populations. These data showed that mouse and human germinal centre B cells shared similar transcriptional features, whereas mouse B1 B cells were distinct from proposed human B1 B cells.

Keywords: B cells; meta-analysis; microarray; transcriptomics.

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Figures

Figure 1

Data analysis pipeline used in the current study.

Figure 2

Clustering of samples based on their global gene expression profile. A Pearson correlation matrix was prepared by comparing data derived from all 84 samples. A network graph was then constructed using sample-to-sample relationships greater than r ≥ 0·85, and clustered using a Markov Clustering inflation value of 2·2. Here, the nodes represent samples (individual micro-array data sets) and each cluster of nodes is assigned a different colour. The edges represent the connections between data sets and are coloured according to the strength of the correlation (red, r = 1·0; blue, r ≥ 0·85). Full descriptions of the sources of each data set are given in Table S1. BM, bone marrow; FL, fetal liver; LN, lymph node; MLN, mesenteric lymph node; PC, peritoneal cavity; SPL, spleen.

Figure 3

Network analysis of mouse B-cell subset transcriptomics data. (a) Main component of the network graph derived from 84 micro-array data sets of distinct mouse B-cell subsets. Here, the nodes represent probe sets (genes) and the edges represent correlations between individual expression profiles above r ≥ 0·85. (b) The mean expression profiles of the genes in selected clusters across the 84 samples. _x_-axis shows the samples, grouped according to cell type (in order of presentation in Table S1). For each cell population mean expression levels are presented and the number of replicates indicated in parenthesis on the _x_-axis. _y_-axis shows the mean signal expression intensity for the cluster (probe set intensity).

Figure 4

Analysis of the genes within clusters 13 and 172 which were expressed specifically by B1 B cells. (a) The mean expression profile of all the probe set intensities within clusters 13 (blue) and 172 (red) over the 84 samples. (b) Heat map showing the mean expression levels of probe sets of interest in clusters 13 and 172. Each column represents the mean (log2) probe set intensity for all samples from each source. Significant differences between groups were sought by analysis of variance. _P_-values for those genes that were expressed significantly (P < 0·05) by B1 B cells at levels > 2·0 fold when compared with the other cell populations. (c) The mean expression profile of probe sets representing Ctla4 (green), Cd80 (red and blue) and Tnfrsf8 (purple) across the 84 samples. (d) Comparison of the mean expression profile of probe sets representing Ciita (blue) and Zbtb32 (red) across the 84 samples. (a–d) Samples are grouped according to cell type and are arranged in order of presentation as listed in Table S1. For each cell population mean expression levels are presented and the number of replicates is indicated in parenthesis on the _x_-axis. Red-boxed area indicates the B1 B-cell data sets. (e) Cartoon illustrating the putative functions of all the genes represented in cluster 13 (black font) and 172 (blue font) in B1 B cells. These genes were then classified into groupings of related cellular function based on published data from literature searches and bioinformatics data bases.

Figure 5

Analysis of the genes within cluster 29 which were expressed specifically by B1a B cells. (a) The mean expression profile of all the probe set intensities within cluster 29 across the 84 samples. (b) Heat map showing the mean expression intensity of each probe set in cluster 29. Each column represents the mean (log2) probe set intensity for all samples from each source. Significant differences between groups were sought by analysis of variance. _P_-values for those genes that were expressed significantly (P < 0·05) by B1a B cells at levels > 2·0-fold when compared with the other cell populations. (a, b) Samples are grouped according to cell type and are arranged in order of presentation as listed in Table S1. For each cell population mean expression levels are presented and the number of replicates is indicated in parenthesis on the _x_-axis. Red-boxed area indicates the B1a B-cell data sets. (c) Cartoon illustrating the putative functions of all the genes represented in cluster 29 in B1a B cells.

Figure 6

Analysis of the genes within cluster 45 with expression enriched in B1 B cells and marginal zone (MZ) B cells. (a) The mean expression profile of all the probe set intensities within cluster 45 over the 84 samples. (b) Heat map showing the mean expression intensity of each probe set in cluster 45. Each column represents the mean (log2) probe set intensity for all samples from each source. Significant differences between groups were sought by analysis of variance. _P_-values for those genes that were expressed significantly (P < 0·05) by B1 B cells and MZ B cells at levels > 2·0-fold when compared with the other cell populations. (c) The mean expression profile of probe sets representing Atxn1 (blue and red) and Bhlhe41 (green) across the 84 samples. (d) Comparison of the mean expression profile of probe sets representing Cnr2 (blue), Gpr55 (red) and Tbc1d9 (green) across the 84 samples. (a–d) Samples are grouped according to cell type and are arranged in order of presentation as listed in Table S1. For each cell population mean expression levels are presented and the number of replicates is indicated in parenthesis on the _x_-axis. Red-boxed area indicates the B1 B-cell and MZ B-cell data sets. (e) Cartoon illustrating the putative functions of all the genes represented in cluster 45 in B1 B cells and MZ B cells.

Figure 7

Analysis of the genes within cluster 39 with expression enriched in marginal zone (MZ) B cells. (a) The mean expression profile of all probe set intensities within cluster 39 over the 84 samples. (b) Heat map showing the mean expression intensity of each probe set in cluster 39. Each column represents the mean (log2) probe set intensity for all samples from each source. Significant differences between groups were sought by analysis of variance. P_-values for those genes that were expressed significantly (P < 0·05) by MZ B cells at levels > 2·0 fold when compared with the other cell populations. (c) The mean expression profile of probe sets representing S1pr1 (blue), S1pr2 (red) and S1pr3 (green) across the 85 samples. (d) Treatment of mice with the S1P receptor modulator FTY720 rapidly displaces MZ B cells (CD1d+ cells, red) from the splenic MZ. In control mice many MZ B cells (left-hand panel, arrow) are situated within the MZ adjacent to the ring of MADCAM1-expressing sinus-lining cells (green). Following treatment with FTY720 MZ B cells are displaced from the MZ and retained in the follicles (right-hand panel, arrow-heads). FO, B-cell follicle. (e) Comparison of the mean expression profile of probe sets representing Adam28 (light blue), Asb2_ (red), Tspan15 (green) and Zc3h12c (dark blue) across the 85 samples. (a, b, c and e) Samples are grouped according to cell type and are arranged in order of presentation as listed in Table S1. For each cell population mean expression levels are presented and the number of replicates is indicated in parenthesis on the _x_-axis. Red-boxed area indicates the MZ B-cell data sets. Blue-boxed area in (e) indicates the germinal centre (GC) B-cell data sets. (f) Cartoon illustrating the putative functions of all the genes represented in cluster 39 in MZ B cells.

Figure 8

Analysis of the genes within cluster 37 with expression enriched in recirculating, transitional and B2 B cells. (a) The mean expression profile of all the probe set intensities within cluster 37 over the 84 samples. (b) Heat map showing the mean expression intensity of each probe set in cluster 37. Each column represents the mean (log2) probe set intensity for all samples from each source. Significant differences between groups were sought by analysis of variance. _P_-values for those genes that were expressed significantly (P < 0·05) by recirculating, transitional and B2 B cells at levels > 2·0-fold when compared with the other cell populations. (c) The mean expression profile of Fcer2a across the 84 samples. (d) Comparison of the mean expression profile of probe sets representing Gdf11 (red), Icosl (green), Lrrk2 (dark blue) and Mef2c (light blue) across the 84 samples. (a–d) Samples are grouped according to cell type and are arranged in order of presentation as listed in Table S1. For each cell population mean expression levels are presented and the number of replicates is indicated in parenthesis on the _x_-axis. Red-boxed areas indicate the recirculating, transitional and B2 B cells data sets. (e) Cartoon illustrating the putative functions of all the genes represented in cluster 45 in recirculating, transitional and B2 B cells.

Figure 9

Analysis of the genes within cluster 20 with expression enriched in germinal centre (GC) B cells. (a) The mean expression profile of all probe set intensities within cluster 29 over the 84 samples. (b) Heat map showing the mean expression intensity of each probe set in cluster 29. Each column represents the mean (log2) probe set intensity for all samples from each source. Significant differences between groups were sought by analysis of variance. _P_-values for those genes that were expressed significantly (P < 0·05) by recirculating, transitional and B2 B cells at levels > 2·0-fold when compared with the other cell populations. (a, b) Samples are grouped according to cell type and are arranged in order of presentation as listed in Table S1. For each cell population mean expression levels are presented and the number of replicates is indicated in parenthesis on the _x_-axis. Red-boxed areas indicate the GC B-cell data sets. (c) Cartoon illustrating the putative functions of all the genes represented in cluster 20 in recirculating, transitional and B2 B cells.

References

1. Theocharidis A, van Dongen S, Enright AJ, Freeman TC. Network visualisation and analysis of gene expression data using Biolayout Express3D. Nat Protoc. 2009;4:1535–50. -PubMed
1. Freeman TC, Goldovsky L, Brosch M, et al. Construction, visualisation, and clustering of transcriptional networks from microarray expression data. PLoS Comput Biol. 2007;3:2032–42. -PMC -PubMed
1. Hume DA, Summers KM, Raza S, Baillie JK, Freeman TC. Functional clustering and lineage markers: insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations. Genomics. 2010;95:328–38. -PubMed
1. Mabbott NA, Baillie JC, Hume DA, Freeman TC. Meta-analysis of co-expressed gene signatures in mouse leukocyte populations. Immunobiology. 2010;215:724–36. -PubMed
1. Kobayashi A, Donaldson DS, Kanaya T, et al. Identification of novel genes selectively expressed in the follicle-associated epithelium from the meta-analysis of transcriptomics data from multiple mouse cell and tissue populations. DNA Res. 2012;19:407–22. -PMC -PubMed

Identification of co-expressed gene signatures in mouse B1, marginal zone and B2 B-cell populations - PubMed (original) (raw)