Menin regulates the serine biosynthetic pathway in Ewing sarcoma

Abstract

Developmental transcription programs are epigenetically regulated by multi-protein complexes, including the menin- and MLL-containing trithorax (TrxG) complexes, which promote gene transcription by depositing the H3K4me3 activating mark at target gene promoters. We recently reported that in Ewing sarcoma, MLL1 (lysine methyltransferase 2A, KMT2A) and menin are overexpressed and function as oncogenes. Small molecule inhibition of the menin-MLL interaction leads to loss of menin and MLL1 protein expression, and to inhibition of growth and tumorigenicity. Here, we have investigated the mechanistic basis of menin-MLL-mediated oncogenic activity in Ewing sarcoma. Bromouridine sequencing (Bru-seq) was performed to identify changes in nascent gene transcription in Ewing sarcoma cells, following exposure to the menin-MLL interaction inhibitor MI-503. Menin-MLL inhibition resulted in early and widespread reprogramming of metabolic processes. In particular, the serine biosynthetic pathway (SSP) was the pathway most significantly affected by MI-503 treatment. Baseline expression of SSP genes and proteins (PHGDH, PSAT1, and PSPH), and metabolic flux through the SSP were confirmed to be high in Ewing sarcoma. In addition, inhibition of PHGDH resulted in reduced cell proliferation, viability, and tumor growth in vivo, revealing a key dependency of Ewing sarcoma on the SSP. Loss of function studies validated a mechanistic link between menin and the SSP. Specifically, inhibition of menin resulted in diminished expression of SSP genes, reduced H3K4me3 enrichment at the PHGDH promoter, and complete abrogation of de novo serine and glycine biosynthesis, as demonstrated by metabolic tracing studies with C-labeled glucose. These data demonstrate that the SSP is highly active in Ewing sarcoma and that its oncogenic activation is maintained, at least in part, by menin-dependent epigenetic mechanisms involving trithorax complexes. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley& Sons, Ltd.

Upregulation of phosphoserine phosphatase contributes to tumor progression and predicts poor prognosis in non‐small cell lung cancer patients

“…Previous studies have shown that high PSPH expression in many cancers is significantly related to poor prognosis, positive metastasis, and high clinicopathologic stage, including colorectal cancer, phyllodes tumor, breast cancer, Ewing sarcoma, and hepatocellular carcinoma . For example, PSPH contributes to cell survival and proliferation by interacting with c‐MYC under glucose/glutamine deprivation conditions in hepatocellular carcinoma .…”

Meta-analysis of targeted metabolomics data from heterogeneous biological samples provides insights into metabolite dynamics

“…Preparation of the sample types below has been described before Schofield et al, 2018;Sousa et al, 2016;Svoboda et al, 2018;Yuan et al, 2012). A brief description follows.…”

“…It utilizes both RPLC and HILIC methods with dynamic MRM (dMRM) as a means to maximize the coverage and sensitivity of target metabolites. Together with our customized computational and statistical analysis pipeline, this platform has been recently applied in several biological contexts Schofield et al, 2018;Sousa et al, 2016;Svoboda et al, 2018). Herein, we report heterogeneous data sets from a wide range of experiments and sample types that were generated on our LC-MS/MS targeted metabolomics platform over a period of one year.…”

Molecular genetics of Ewing sarcoma, model systems and finding novel (immuno-) therapeutic targets

“…Fusion of the N-terminal region of EWSR1, which contains a strong transcriptional activation domain [21,22] , and these DNA binding domains causes aberrant transcription of a multitude of genes. Additionally, EWSR1-ETS is known to affect epigenetic programs [23,24] , splicing [25,26] , and metabolic activity [27] of EWS. Oncogenic fusions between ETS genes and transcriptional activators are not unique to EWS: in 50%-70% of prostate cancers, similar chromosomal rearrangements are found [28] .…”

“…Targeting the fusion protein directly has proven to be challenging due to its flexibility, but progress has been made and a phase I clinical trial (NCT02657005) is ongoing with a small molecule inhibitor [108] . Aside from targeting the EWSR1-ETS fusion protein directly, inhibiting its dominant direct targets has been investigated as therapeutic alternative, as EWSR1-ETS is a key driver in the epigenetics [23,24] , transcription [109] , splicing [25,26] , and metabolic [27] reprogramming of EWSR1-ETS.…”