Transcriptional circuits in B cell transformation

Abstract

Purpose of review: Loss of IKAROS in committed B cell precursors causes a block in differentiation while at the same time augments aberrant cellular properties, such as bone marrow stromal adhesion, self-renewal and resistance to glucocorticoid-mediated cell death. B cell acute lymphoblastic leukaemias originating from these early stages of B cell differentiation and associated with IKAROS mutations share a high-risk cellular phenotype suggesting that deregulation of IKAROS-based mechanisms cause a highly malignant disease process.

Recent studies: Recent studies show that IKAROS is critical for the activity of super-enhancers at genes required for pre-B cell receptor (BCR) signalling and differentiation, working either downstream of or in parallel with B cell master regulators such as EBF1 and PAX5. IKAROS also directly represses a cryptic regulatory network of transcription factors prevalent in mesenchymal and epithelial precursors that includes YAP1, TEAD1/2, LHX2 and LMO2, and their targets, which are not normally expressed in lymphocytes. IKAROS prevents not only expression of these 'extra-lineage' transcription factors but also their cooperation with endogenous B cell master regulators, such as EBF1 and PAX5, leading to the formation of a de novo for lymphocytes super-enhancer network. IKAROS coordinates with the Polycomb repression complex (PRC2) to provide stable repression of associated genes during B cell development. However, induction of regulatory factors normally repressed by IKAROS starts a feed-forward loop that activates de-novo enhancers and elevates them to super-enhancer status, thereby diminishing PRC2 repression and awakening aberrant epithelial-like cell properties in B cell precursors.

Summary: Insight into IKAROS-based transcriptional circuits not only sets new paradigms for cell differentiation but also provides new approaches for classifying and treating high-risk human B-ALL that originates from these early stages of B cell differentiation.

Figure 1. Developmental progression from HSC to immature B cell

Expression of cell surface markers that define discrete stages of B cell differentiation in mouse and human are shown together with Igh and Igk gene rearrangements. The stage-specific arrest in differentiation caused by mouse genetic mutations in transcription and signaling factors is shown as red perpendicular lines on the developmental progression. Germ-line deletion of Ikzf1 arrest lymphocyte differentiation at the LMPP stage, whereas, conditional inactivation of Ikzf1 downstream of the LMPP arrests at the large pre-B stage. IKAROS deficient large pre-B cells exhibit leukemic potential upon transplantation into a NOD/SCID host. Surface phenotype of human B-ALL and its origins from the early stages of B cell differentiation are shown. Loss of IKAROS augments integrin signaling, weak stromal adhesion properties and self-renewal normally displayed by wild type large pre-B cells.

Figure 2. Repression of niche-interactions from the HSC to the large pre-B cell

Comparative analysis of genes that were previously shown to be up-regulated upon loss of IKAROS in the HSC, LMPP and large pre-B cell [23,24]. A circos diagram depicting overlap between up-regulated genes (purple connecting lines) in IKAROS deficient HSC, LMPP and large pre-B cells is shown on the left side. A heatmap of functional pathways supported by the IKAROS-repressed genes in these cell types is shown on the right side. The color intensity of the heatmap is a measure of the p-value that indicates the enrichment for a given pathway in the corresponding list of up-regulated genes provided by a given experimental condition (e.g. in HSC, LMPP or large pre-B cell)

Figure 3. Reciprocal regulation of enhancers and B cell lineage fidelity

IKAROS sets a highly permissive chromatin environment that defines super-enhancers at genes involved in pre-BCR signaling and differentiation. IKAROS also associates with the inactive enhancers of genes that support pathways such as cell adhesion, self-renewal and drug resistance normally affiliated with a non-lymphoid cell identity. Among the repressed IKAROS gene targets are master transcription regulators prevalent in non-lymphoid cells that upon IKAROS loss become induced and co-operate with B cell transcription factors to activate a de novo super-enhancer repertoire that supports the aberrant cellular properties of the mutant B cell precursors. Notably, these aberrant properties manifested in primary IKAROS pre-B cells are likely responsible for the high-risk status of leukemias caused by activating mutations in tyrosine kinases (e.g. BCR-ABL, JAK2-PDGFR).

Figure 4. A hybrid “extra-lineage-B cell” transcription factor network is responsible for the IKAROS loss-of-function genetic effects

The knockdown effect of individual “extra-lineage” and B cell transcription factors on genes up-regulated in IKAROS deficient large pre-B cells is shown. A circos diagram depicting the overlap of YAP1, EBF1, LMO2 and LHX2 on inducing the genes up-regulated (connected purple lines) in IKAROS deficient pre-B cells is shown. The effect on up-regulated functional pathways associated with these genes is also shown (connected light blue lines) in the same diagram. A heatmap of functional pathways supported by the normally IKAROS-repressed genes and their dependency on YAP1, EBF1, LMO2 and LHX2 for expression is shown on the right side (as described in Figure 2).