Supplementary Figures 1-6 from Oncogenic Gene-Expression Programs in Leiomyosarcoma and Characterization of Conventional, Inflammatory, and Uterogenic Subtypes
posted on 2023-04-03, 19:43authored byMatthew L. Hemming, Changyu Fan, Chandrajit P. Raut, George D. Demetri, Scott A. Armstrong, Ewa Sicinska, Suzanne George
Figure S1. Smooth muscle enriched gene sets and tumor suppressors in LMS. Figure S2. A unique subset of genes differentiates molecular subtypes of LMS. Figure S3. Validation of LMS subtypes in separate cohorts. Figure S4. Expression of previously described differentiating transcripts in LMS subtypes. Figure S5. Kaplan-Meier analysis of LMS subtypes. Figure S6. LMS cell lines lack an LMS-related gene expression program.
Funding
Erica's Entourage Sarcoma Epigenome Project Fund
Leiomyosarcoma Support and Direct Research Foundation
Catherine England Leiomyosarcoma Fund
Sarcoma Foundation of America
Shore Fellowship Program
Harvard Catalyst Medical Research
NIH
History
ARTICLE ABSTRACT
Leiomyosarcoma (LMS) is a mesenchymal neoplasm with complex copy-number alterations and characteristic loss of tumor suppressor genes without known recurrent activating mutations. Clinical management of advanced LMS relies on chemotherapy and complementary palliative approaches, and research efforts to date have had limited success identifying clinically actionable biomarkers or targeted therapeutic vulnerabilities. To explore the biological underpinning of LMS, we evaluated gene-expression patterns of this disease in comparison with diverse sarcomas, nonmesenchymal neoplasms, and normal myogenic tissues. We identified a recurrent gene-expression program in LMS, with evidence of oncogenic evolution of an underlying smooth-muscle lineage-derived program characterized by activation of E2F1 and downstream effectors. Recurrently amplified or highly expressed genes in LMS were identified, including IGF1R and genes involved in retinoid signaling pathways. Though the majority of expressed transcripts were conserved across LMS samples, three separate subtypes were identified that were enriched for muscle-associated transcripts (conventional LMS), immune markers (inflammatory LMS), or a uterine-like gene-expression program (uterogenic LMS). Each of these subtypes expresses a unique subset of genes that may be useful in the management of LMS: IGF1R was enriched in conventional LMS, worse disease-specific survival was observed in inflammatory LMS, and prolactin was elaborated by uterogenic LMS. These results extend our understanding of LMS biology and identify several strategies and challenges for further translational investigation.
LMS has a recurrent oncogenic transcriptional program and consists of molecular subtypes with biological and possible clinical implications.