A quantitative proteomics approach identifies ETV6 and IKZF1 as new regulators of anERG-driven transcriptional network

Abstract

Aberrant stem cell-like gene regulatory networks are a feature of leukaemogenesis. The ETS-related gene (ERG), an important regulator of normal haematopoiesis, is also highly expressed in T-ALL and acute myeloid leukaemia (AML). However, the transcriptional regulation of ERG in leukaemic cells remains poorly understood. In order to discover transcriptional regulators of ERG, we employed a quantitative mass spectrometry-based method to identify factors binding the 321 bp ERG +85 stem cell enhancer region in MOLT-4 T-ALL and KG-1 AML cells. Using this approach, we identified a number of known binders of the +85 enhancer in leukaemic cells along with previously unknown binders, including ETV6 and IKZF1. We confirmed that ETV6 and IKZF1 were also bound at the +85 enhancer in both leukaemic cells and in healthy human CD34+ haematopoietic stem and progenitor cells. Knockdown experiments confirmed that ETV6 and IKZF1 are transcriptional regulators not just of ERG, but also of a number of genes regulated by a densely interconnected network of seven transcription factors. At last, we show that ETV6 and IKZF1 expression levels are positively correlated with expression of a number of heptad genes in AML and high expression of all nine genes confers poorer overall prognosis.

An ERG Enhancer–Based Reporter Identifies Leukemia Cells with Elevated Leukemogenic Potential Driven by ERG-USP9X Feed-Forward Regulation

“…Our results demonstrate that ERGþ85 reporter activity varies among Jurkat cells, which is consistent with the highly dynamic nature of the TF network interacting with this genomic element (64)(65)(66). Positive and negative feedback loops that can reinforce or diminish TF expression (and thus stabilize ERGþ85 Neg or ERGþ85 High states) are general phenomenon in the developmental TF networks (67).…”

T cell epigenetic remodeling and accelerated epigenetic aging are linked to long-term immune alterations in childhood cancer survivors

“…Plasma samples (14ul) from childhood cancer survivors were depleted from the 14 most abundant proteins (Sigma Seppro IgY14 Spin columns). Depleted plasma sample and conditioned media from cultured fibroblasts and fibroblasts differentiated into adipocytes (only 0/3Gy and at 24 h/7 days post-irradiation) were processed as previously described with slight modifications (see “Additional file 1 ”) [ 45 ]. A survey scan m / z 350–1750 was acquired in the Orbitrap and lock mass enabled with data-dependent tandem MS analysis performed using a top-speed approach (cycle time of 2 s).…”

Acute myeloid leukemia carrying ETV6 mutations: biologic and clinical features

“…Previous studies have also suggested that ETV6 mutations usually associated with NPM1 mutations (The role of etv6 together with other genes in the development of leukaemia will be discussed later in this article) [20]. We thus suspect that ETV6 mutations may cooperate with other mutations to establish their own network structure, driving the self-renewal of leukaemia stem cells, thereby promoting the development of leukaemia.…”