Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) are the two most common non-Hodgkin lymphomas (NHLs). Here we sequenced tumour and matched normal DNA from 13 DLBCL cases and one FL case to identify genes with mutations in B-cell NHL. We analysed RNA-seq data from these and another 113 NHLs to identify genes with candidate mutations, and then re-sequenced tumour and matched normal DNA from these cases to confirm 109 genes with multiple somatic mutations. Genes with roles in histone modification were frequent targets of somatic mutation. For example, 32% of DLBCL and 89% of FL cases had somatic mutations in MLL2, which encodes a histone methyltransferase, and 11.4% and 13.4% of DLBCL and FL cases, respectively, had mutations in MEF2B, a calcium-regulated gene that cooperates with CREBBP and EP300 in acetylating histones. Our analysis suggests a previously unappreciated disruption of chromatin biology in lymphomagenesis

The regulatory landscape of the glioma-associated transcription factor Capicua

The metazoan developmental gene capicua transcriptional repressor (CIC) encodes a transcription factor that transduces receptor tyrosine kinase signaling into gene expression changes. Aberrant CIC function is implicated in oligodendroglioma (ODG) development since one CIC allele is lost while the other is mutated in ~70% of ODGs. We therefore investigated how CIC can affect gene expression at a genome-wide level by inactivating CIC in HEK293a cells and subsequently measuring gene expression changes using microarrays. From this, gene expression changes spanning entire chromosomes were detected. Additionally, 24 candidate CIC-regulated genes were identified in HEK293a cells that also have evidence of CIC-dependent regulation in ODGs sequenced by The Cancer Genome Atlas (TCGA). Of these 24 genes, 5 genes (CNTFR, DUSP6, GPR3, SHC3, and SPRY4) with reported functions in mitogen-activated protein kinase (MAPK) signaling and central nervous system (CNS) development were further validated to undergo CIC-dependent regulation in HeLa cells. Finally, investigating how different CIC mutations affect gene expression revealed that different types of ODG-associated CIC mutations either abrogated or potentially preserved CIC’s transcriptionally repressive activity. These findings shed insight into possible roles for CIC in regulating gene expression at a chromosome-wide scale, MAPK signaling, CNS development, and ODG development.Science, Faculty ofGraduat