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BCAT1 and miR-2504: novel methylome signature distinguishes spindle/desmoplastic melanoma from superficial malignant peripheral nerve sheath tumor

ABSTRACT: Genome wide methylation of superficial malignant peripheral nerve sheath tumors and spindle cell melanomas. EPIC HD 850K array is used to identifiy differentally methylated promoter region probes and unique methyome signatures. Superficial/cutaneous malignant peripheral nerve sheath tumor (c-MPNST) is a rare, soft tissue neoplasm that shares morphological, immunohistochemical and molecular with spindle and desmoplastic melanoma (SDM). Herein we investigate a methylome signature distinguishing between both entities. DNA from formalin-fixed, paraffin-embedded (FFPE) tissues was extracted and processed using the Illumina Infinium epic array interrogating 866,562 CpG sites. Using a home grown informatics pipeline we identify differentially methylated regions (DMR) between both entities. Functional network analysis for enrichment signatures was performed using DAVID tools. Identified DMR’s are compared with TCGA skin cutaneous melanoma (SKCM) data and a recently published set of MPNST in order to assess specifity of the identified signature. Thirty patients are included (SDM= 15 and c-MPNST=15) including 23 males and 7 females. Unsupervised hierarchical clustering probes showed a distinct pattern of methylation between c-MPNST and SDM. Two probes cg20783223 and cg13332552 co-localized in the promoter region of BCAT1 and MIR2504. Pathway analysis highlighted an enrichment in s subset of genes involved in breast and gastric cancer centered on BCAT1 and downstream activated genes in the mTORC pathway. Our study identifies BCAT1 as a unique marker distinguishing between SDM and MPNST. Further immunohistochemical studies are underway to investigate the role of BCAT expression in that regard.

ORGANISM(S): Homo sapiens

PROVIDER: GSE112308 | GEO | 2018/09/10

REPOSITORIES: GEO

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Project description:The branched-chain amino acid (BCAA) pathway and high levels of BCAA transaminase 1 (BCAT1) have recently been associated with aggressiveness in several cancer entities. However, the mechanistic role of BCAT1 in this process remains largely uncertain. Here, by performing high-resolution proteomic analysis of human acute myeloid leukaemia (AML) stem-cell and non-stem-cell populations, we find the BCAA pathway enriched and BCAT1 protein and transcripts overexpressed in leukaemia stem cells. We show that BCAT1, which transfers α-amino groups from BCAAs to α-ketoglutarate (αKG), is a critical regulator of intracellular αKG homeostasis. Further to its role in the tricarboxylic acid cycle, αKG is an essential cofactor for αKG-dependent dioxygenases such as Egl-9 family hypoxia inducible factor 1 (EGLN1) and the ten-eleven translocation (TET) family of DNA demethylases. Knockdown of BCAT1 in leukaemia cells caused accumulation of αKG, leading to EGLN1-mediated HIF1α protein degradation. This resulted in a growth and survival defect and abrogated leukaemia-initiating potential. By contrast, overexpression of BCAT1 in leukaemia cells decreased intracellular αKG levels and caused DNA hypermethylation through altered TET activity. AML with high levels of BCAT1 (BCAT1high) displayed a DNA hypermethylation phenotype similar to cases carrying a mutant isocitrate dehydrogenase (IDHmut), in which TET2 is inhibited by the oncometabolite 2-hydroxyglutarate11,12. High levels of BCAT1 strongly correlate with shorter overall survival in IDHWTTET2WT, but not IDHmut or TET2mutAML. Gene sets characteristic for IDHmut AML13 were enriched in samples from patients with an IDHWTTET2WTBCAT1high status. BCAT1highAML showed robust enrichment for leukaemia stem-cell signatures14,15, and paired sample analysis showed a significant increase in BCAT1 levels upon disease relapse. In summary, by limiting intracellular αKG, BCAT1 links BCAA catabolism to HIF1α stability and regulation of the epigenomic landscape, mimicking the effects of IDH mutations. Our results suggest the BCAA–BCAT1–αKG pathway as a therapeutic target to compromise leukaemia stem-cell function in patients with IDHWTTET2WT AML.

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BCAT1 and miR-2504: novel methylome signature distinguishes spindle/desmoplastic melanoma from superficial malignant peripheral nerve sheath tumor

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