Signatures of murine B-cell development implicate Yy1 as a regulator of the germinal center-specific program

Abstract

We utilized gene expression profiling of a comprehensive panel of purified developmentally defined normal murine B cells to identify unique transcriptional signatures for each subset. To elucidate transcription factor activities that function in a stage-specific fashion, we used gene sets that share transcription factor targets and found that germinal center B cells had a robust enrichment of up-regulated and down-regulated signatures compared with the other B-cell subsets. Notably, we found Yy1 and its targets to be central regulators of the germinal center B (GCB)-specific transcriptional program with binding of Yy1 to select signature genes in GCB cells, and translation of the Yy1 signatures to human GCB cells. We then tested whether our newly generated, stage-specific transcriptional signatures could be used to link murine lymphoma models to stages of normal B-cell development. Although each of the molecularly defined murine lymphoma models conserved certain stage-specific features of normal B-cell development, there was a significant alteration of the normal differentiation signature following malignant transformation. These findings offer important tools and insights for elucidating differences between normal and malignant B cells.

Fig. 1.

Unsupervised clustering of B-cell subsets. Unsupervised hierarchical clustering of individual samples within the space of the 3,000 most variably expressed genes (Left) resulted in cosegregation of samples with those of the same or similar differentiation state, as shown by the enlargement of the clustering dendogram (Right).

Fig. 2.

Distinct transcriptional signatures of B-cell subsets. Signatures consisting of 350 significantly (FDR < 0.25) up-regulated and 350 significantly down-regulated genes were defined and are shown for each subset.

Fig. 3.

Signatures implicate Yy1 as a GCB-specific transcriptional regulator. (A) HG-GSEA of the GCB-specific signature and the enrichment of target gene sets for Yy1 (Top), Creb (Middle), and E2f (Bottom). Each point represents the FDR of an independent gene set within a specific B-cell subset signature. (B) GCB-specific genes within Yy1 target gene sets. Creb and E2F target gene sets are indicated by gray and black circles to the left of gene symbols, respectively. The subset of Yy1 target genes validated by ChIP-qPCR are indicated at Bottom. (C) ChIP-qPCR of GCB-specific Yy1 target genes. (D) Distribution frequency of the Yy1 binding-sequence motif (Top Right) enriched in the GCB signature. (E) GSEA of the 125 murine GCB-specific Yy1 target genes (identified by motif analysis) in human GCB vs. non–GCB-cell transcriptional profiles.

Fig. 4.

Enrichment of normal B-cell signatures in murine lymphoma models. (A) Classification signatures of the normal murine B-cell subsets. (B) Transcriptional signatures of the murine tumor models. (C) HG-GSEA of normal B-cell classification signatures (A) within tumor model signatures (B). The enrichment of the signatures of normal B-cell subsets with which the tumor models are putatively aligned is shown.