Cooperative Super-Enhancer Inactivation through Loss of Crebbp and KMT2D Skews B Cell Fate Decisions and Yields T Cell-Depleted Lymphomas

Abstract

Mutations in chromatin modifiers are a hallmark of many tumors, especially lymphomas arising from germinal center (GC) B cells. Given that most of these lymphoma mutations induce aberrant gene repression, it is surprising that they often co-occur in individual patients. The most common pairing are mutations affecting CREBBP and KMT2D, even though regulating overlapping gene enhancers and pathways. Hence their co-occurrence is especially puzzling. Herein, we report that combined haploinsufficiency of Crebbp and Kmt2d (C+K) do indeed induce a more severe lymphoma phenotype (vs either allele alone) and unexpectedly conferred an immune evasive phenotype manifesting as reduced CD8+ T cell infiltration. This was linked to profound repression of immune synapse genes that provide costimulatory effects to T-cells and others. Repression of immune synapse genes was reflected in impaired response to T-cell directed cell fate decisions and weakening of costimulatory signals. From the epigenetic perspective we observed interaction and mutually dependent cooperative binding of C+K to chromatin. Notably loss of C+K cooperativity was selectively severe at superenhancers (vs enhancers), especially those driving expression of immune synapse signaling genes and pointing to a particular dependency for both co-activators at these specialized regulatory elements. Therefore, we show that critical features of the lymphoma microenvironment are shaped by specific combinations of chromatin modifier somatic mutations, induced by the dependency of immune synapse superenhancers on cooperative actions of CREBBP and KMT2D.