Epigenomic and Transcriptomic Profiling of Solitary Fibrous Tumors Identifies Site-Specific Patterns and Candidate Genes Regulated by DNA Methylation

Authors

Hannah C Beird
Jeffrey M Cloutier
Nalan Gokgoz
Christopher Eeles
Anthony M Griffin
Davis R Ingram
Khalida M Wani
Rossana Lazcano Segura
Luca Cohen
Carl Ho
Jay S Wunder
Irene L Andrulis
P Andrew Futreal
Benjamin Haibe-Kains
Alexander J Lazar
Wei-Lien Wang
Joanna Przybyl
Elizabeth G Demicco

Language

English

Publication Date

11-1-2024

Journal

Laboratory Investigation

DOI

10.1016/j.labinv.2024.102146

PMID

39357799

Abstract

A solitary fibrous tumor (SFT) is a rare mesenchymal neoplasm that can arise at any anatomical site and is characterized by recurrent NAB2::STAT6 fusions and metastatic progression in 10% to 30%. The cell of origin has not been identified. Despite some progress in understanding the contribution of heterogeneous fusion types and secondary mutations to SFT biology, epigenetic alterations in extrameningeal SFT remain largely unexplored, and most sarcoma research to date has focused on the use of methylation profiling for tumor classification. We interrogated genome-wide DNA methylation in 79 SFTs to identify informative epigenetic changes. RNA-seq data from targeted panels and data from The Cancer Genome Atlas (TCGA) were used for orthogonal validation of selected findings. In unsupervised clustering analysis, the top 500 most variable cytosine-guanine sites segregated SFTs by primary anatomical site. Differentially methylated genes associated with the primary SFT site included EGFR; TBX15; multiple HOX genes; and their cofactors EBF1, EBF3, and PBX1; as well as RUNX1 and MEIS1. Of the 20 DMGs interrogated on the RNA-seq panel, 12 were significantly differentially expressed according to site. However, except TBX15, most of these also showed differential expression according to NAB2::STAT6 fusion type, suggesting that the fusion oncogene contributes to the transcriptional regulation of these genes. Transcriptomic data confirmed an inverse correlation between gene methylation and the expression of TBX15 in both SFT and TCGA sarcomas. TBX15 also showed differential mRNA expression and 5' UTR methylation between tumors in different anatomical sites in TCGA data. In all analyses, TBX15 methylation and mRNA expression retained the strongest association with tissue of origin in SFT and other sarcomas, suggesting a possible marker to distinguish metastatic tumors from new primaries without genomic profiling. Epigenetic signatures may further help to identify SFT progenitor cells at different anatomical sites.

Keywords

Solitary Fibrous Tumors, Epigenomics, Repressor Proteins, STAT6 Transcription Factor, Gene Expression Regulation, Neoplastic, Oncogene Fusion, RNA-Seq, T-Box Domain Proteins, 5' Untranslated Regions, Humans, Male, Female, Adolescent, Young Adult, Adult, Middle Aged, Aged, Aged, 80 and over, Retrospective Studies, Prospective Studies, Biopsy, Epigenesis, Genetic, HOX, NAB2::STAT6, RNA-seq, TBX15, fusion, methylation profiling, solitary fibrous tumor, telomerase reverse transcriptase

Published Open-Access

yes

Recommended Citation

Beird, Hannah C; Cloutier, Jeffrey M; Gokgoz, Nalan; et al., "Epigenomic and Transcriptomic Profiling of Solitary Fibrous Tumors Identifies Site-Specific Patterns and Candidate Genes Regulated by DNA Methylation" (2024). Faculty, Staff and Student Publications. 5673.
https://digitalcommons.library.tmc.edu/uthgsbs_docs/5673