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

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. Two sets of tumors including 15 MPNST and 15 SDM's are analyzed.

本研究针对浅表皮恶性周围神经鞘瘤与梭形细胞黑色素瘤开展全基因组甲基化分析，采用EPIC HD 850K芯片（EPIC HD 850K array）鉴定差异甲基化启动子区域探针及独特甲基化组特征。

浅表皮/皮肤恶性周围神经鞘瘤（cutaneous malignant peripheral nerve sheath tumor, c-MPNST）是一类罕见软组织肿瘤，其形态学、免疫组化及分子特征与梭形细胞促纤维增生性黑色素瘤（spindle and desmoplastic melanoma, SDM）高度相似。本研究旨在鉴定可区分这两类肿瘤的甲基化组特征。研究提取福尔马林固定石蜡包埋（FFPE）组织的基因组DNA，采用Illumina Infinium EPIC芯片（可检测866562个CpG位点）进行杂交检测。

通过自主研发的生物信息学流程，我们鉴定出两类肿瘤间的差异甲基化区域（differentially methylated regions, DMR）。采用DAVID工具开展富集特征的功能网络分析，并将所鉴定的DMR与癌症基因组图谱（TCGA）皮肤黑色素瘤（SKCM）数据集及近期发表的MPNST数据集进行比对，以评估所获特征的特异性。

本研究共纳入30例患者（SDM 15例，c-MPNST 15例），其中男性23例，女性7例。无监督层次聚类分析显示，c-MPNST与SDM的甲基化探针分布模式存在显著差异。探针cg20783223与cg13332552共定位于BCAT1与MIR2504的启动子区域。通路分析显示，以BCAT1为核心的乳腺癌、胃癌相关基因子集，以及mTORC通路下游激活基因均存在显著富集。

本研究鉴定出BCAT1可作为区分SDM与MPNST的特异性标志物，目前正开展进一步免疫组化研究，以探讨BCAT表达在该鉴别诊断中的作用。本研究共分析两组肿瘤样本，分别包含15例MPNST与15例SDM。