Global Profiling of c-Jun and JunB transcription factor binding sites in an ALK+ ALCL cell line

Abstract

Anaplastic lymphoma kinase-positive, anaplastic large cell lymphoma (ALK+ ALCL) is a T cell lymphoma which features translocations or inversion involving the ALK tyrosine kinase gene, and results in oncogenic fusion proteins (e.g. NPM-ALK). The elevated expression and/or activation of activator protein-1 (AP-1) transcription factors, c-Jun and JunB, is another molecular feature of ALK+ ALCL. c-Jun/JunB transcriptional targets are important in the pathobiology of this lymphoma, and several are also therapeutic targets. To better understand c-Jun/JunB function in ALK+ ALCL, we performed chromatin immunoprecipitation–sequencing experiments in the Karpas 299 ALK+ ALCL cell line to comprehensively identify sites bound by these transcription factors. We identified 13,083 c-Jun and 40,369 JunB binding sites, and ~60% of sites bound by c-Jun were shared with JunB. Many sites were associated with genes known or predicted to be important in the pathogenesis of ALK+ ALCL. Pathway enrichment analysis of genes associated with both c-Jun and JunB binding sites revealed a significant over-representation for pathways associated with cancer and cell signalling. Furthermore, we identified several c-Jun and JunB binding sites associated with the NIBAN2 / FAM129B gene. FAM129B is a PH domain-containing phosphoprotein that promotes proliferation in multiple cell types. However, while we found that FAM129B knock-down resulted in modest cell cycle alteration in most ALK+ ALCL cell lines, this did not appear to result in a significant proliferation defect. Finally, we found that inhibition of NPM-ALK and MEK/Erk signalling altered FAM129B electrophoretic mobility and decreased phosphorylation of FAM129B on serine residues known to be Erk phosphosites. In summary, this study is the first to globally profile sites bound by c-Jun/JunB in ALK+ ALCL. It reveals novel putative targets for these transcription factors in ALK+ ALCL, and identifies FAM129B as a novel phosphoprotein downstream of NPM-ALK signalling.