Intracranial mesenchymal tumors with FET-CREB fusion are composed of at least two epigenetic subgroups distinct from meningioma and extracranial sarcomas

Abstract

'Intracranial mesenchymal tumor, FET-CREB fusion-positive' occurs primarily in children and young adults and has previously been termed intracranial angiomatoid fibrous histiocytoma (AFH) or intracranial myxoid mesenchymal tumor (IMMT). Here we performed genome-wide DNA methylation array profiling of 20 primary intracranial mesenchymal tumors with FET-CREB fusion to further study their ontology. These tumors resolved into two distinct epigenetic subgroups that were both divergent from all other analyzed intracranial neoplasms and soft tissue sarcomas, including meningioma, clear cell sarcoma of soft tissue (CCS), and AFH of extracranial soft tissue. The first subgroup (Group A, 16 tumors) clustered nearest to but independent of solitary fibrous tumor and AFH of extracranial soft tissue, whereas the second epigenetic subgroup (Group B, 4 tumors) clustered nearest to but independent of CCS and also lacked expression of melanocytic markers (HMB45, Melan A, or MITF) characteristic of CCS. Group A tumors most often occurred in adolescence or early adulthood, arose throughout the neuroaxis, and contained mostly EWSR1-ATF1 and EWSR1-CREB1 fusions. Group B tumors arose most often in early childhood, were located along the cerebral convexities or spinal cord, and demonstrated an enrichment for tumors with CREM as the fusion partner (either EWSR1-CREM or FUS-CREM). Group A tumors more often demonstrated stellate/spindle cell morphology and hemangioma-like vasculature, whereas Group B tumors more often demonstrated round cell or epithelioid/rhabdoid morphology without hemangioma-like vasculature, although robust comparison of these clinical and histologic features requires future study. Patients with Group B tumors had inferior progression-free survival relative to Group A tumors (median 4.5 vs. 49 months, p = 0.001). Together, these findings confirm that intracranial AFH-like neoplasms and IMMT represent histologic variants of a single tumor type ('intracranial mesenchymal tumor, FET-CREB fusion-positive') that is distinct from meningioma and extracranial sarcomas. Additionally, epigenomic evaluation may provide important prognostic subtyping for this unique tumor entity.

Keywords: ATF1; CREB1; CREM; EWSR1; angiomatoid fibrous histiocytoma (AFH); brain tumor; clear cell sarcoma; intracranial mesenchymal tumor with FET-CREB fusion; intracranial myxoid mesenchymal tumor; molecular neuropathology; sarcoma.

FIGURE 1

‘Intracranial mesenchymal tumor, FET‐CREB fusion‐positive’ is composed of two distinct epigenetic subgroups. (A) Unsupervised hierarchical clustering of DNA methylation data from 20 intracranial mesenchymal tumors with FET‐CREB fusion showing segregation into two epigenetic subgroups – Group A consisting of 16 tumors and Group B consisting of 4 tumors. Differentially methylated genomic regions between the two subgroups are annotated in Tables S1 and S2. (B) Dot plot of patient age at diagnosis stratified by epigenetic subgroup. (C). Dot plot of tumor anatomic location stratified by epigenetic subgroup. (D) Dot plot of fusion type stratified by epigenetic subgroup. (E). Differential methylation‐based gene ontology analysis for the two epigenetic subgroups of intracranial mesenchymal tumors with FET‐CREB fusion, represented in a bar plot of −log10 p values for the most differentially methylated gene networks

FIGURE 2

Histologic features of intracranial mesenchymal tumors with FET‐CREB fusion belonging to the two epigenetic subgroups. Hematoxylin and eosin‐stained sections from three representative tumors of the two epigenetic subgroups

FIGURE 3

Kaplan‐Meier plot of progression‐free survival for patients with intracranial mesenchymal tumor, FET‐CREB fusion‐positive stratified by epigenetic subgroup

FIGURE 4

tSNE dimensionality reduction plot of genome‐wide DNA methylation profiles from the 20 intracranial mesenchymal tumors with FET‐CREB fusion alongside 210 reference tumors spanning 17 sarcoma and CNS tumor entities previously generated at DKFZ. See Table S4 for tSNE sample manifest. AT/RT, atypical teratoid/rhabdoid tumor. DMG, diffuse midline glioma. DSRCT, desmoplastic small round cell tumor. GBM, glioblastoma. LGFMS, low‐grade fibromyxoid sarcoma. SFT/HPC, solitary fibrous tumor/hemangiopericytoma

FIGURE 5

Epigenetic comparison of Group A intracranial mesenchymal tumors with FET‐CREB fusion to angiomatoid fibrous histiocytoma (AFH) of extracranial soft tissue. (A) Unsupervised hierarchical clustering of DNA methylation data showing segregation of the 16 Group A tumors from 8 reference cases of angiomatoid fibrous histiocytoma arising in extracranial soft tissue. Differentially methylated genomic regions are annotated in Tables S6 and S7. (B) Differential methylation‐based gene ontology analysis for Group A intracranial mesenchymal tumors versus AFH of extracranial soft tissue, represented in a bar plot of −log10 p values for the most differentially methylated gene networks

FIGURE 6

Epigenetic comparison of Group B intracranial mesenchymal tumors with FET‐CREB fusion to clear cell sarcoma (CCS) of extracranial soft tissue. (A) Unsupervised hierarchical clustering of DNA methylation data showing segregation of the 4 Group B tumors from 7 reference cases of clear cell sarcoma arising in extracranial soft tissue. Differentially methylated genomic regions are annotated in Tables S9 and S10. (B) Visualization of DNA methylation status at individual CpG sites (vertical green bars) at the MITF gene locus in the 4 Group B tumors and 7 reference cases of CCS arising in extracranial soft tissue. All but one CpG site demonstrate substantial hypermethylation in the Group B tumors, whereas most all CpG sites are unmethylated or hypomethylated in the CCS tumors. (C) Immunohistochemistry for MITF, a transcription factor robustly expressed in CCS of soft tissue, as well as the other melanocytic markers HMB45 and Melan A, was negative in all four Group B intracranial mesenchymal tumors with FET‐CREB fusion. (D) Differential methylation‐based gene ontology analysis for Group B intracranial mesenchymal tumors versus CCS of extracranial soft tissue, represented in a bar plot of −log10 p values for the most differentially methylated gene networks