Background: Soft tissue sarcomas (STSs) histopathological classification system and the clinical and molecular-based tools that are currently employed to estimate its prognosis have several limitations, impacting prognostication and treatment. Clinically driven molecular profiling studies may cover these gaps and offer alternative tools with superior prognostication capability and enhanced precision and personalized treatment approaches identification ability. Materials and Methods /Results: We performed DNA sequencing (DNA-seq) and RNA sequencing (RNA-seq) to portray the molecular profile of 102 samples of high-grade STS, comprising the three most common STS histotypes. The analysis of RNA-seq data using unsupervised machine learning models revealed previously unknown molecular patterns, identifying four transcriptomic subtypes/clusters (TCs). This TC-based classification has a clear prognostic value (in terms of overall survival (OS) and disease-free survival (DFS)), a finding that was externally validated using independent patient cohorts. The prognostic value of this TC-based classification outperforms the prognostic accuracy of clinical-based (SARCULATOR nomograms) and molecular-based (CINSARC) prognostication tools, being one of the first molecular-based classifications capable of predicting OS in STS. The analysis of DNA-seq data from the same cohort revealed numerous and, in some cases, never documented molecular targets for precision treatment across different transcriptomic subtypes. The functional and predictive value of each genomic variant was analyzed using the Molecular Tumor Board Portal. Conclusions : This newly identified TC-based classification offers a superior prognostic value when compared with current gold-standard clinical and molecular-based prognostication tools, and identifies novel molecular targets for precision treatment, representing a cutting-edge tool for predicting prognosis and guiding treatment across different stages of STS.

Undifferentiated pleomorphic sarcoma (UPS) remains one of the most clinically aggressive and poorly characterized soft-tissue sarcoma subtypes. To uncover distinctive molecular traits for UPS, a multiomics analysis of UPS compared with leiomyosarcoma (LMS) and liposarcoma (LPS) was performed. Transcriptomic profiling revealed that UPS exhibits overexpression of genes encoding succinate dehydrogenase (SDH) subunits, particularly SDHB, SDHC, and SDHD, distinguishing it from LMS and dedifferentiated LPS. This finding was validated using The Cancer Genome Atlas Sarcoma dataset. High SDHB expression in UPS was significantly associated with shorter overall survival, shorter recurrence-free survival, and shorter overall survival from the date of first metastasis. IHC validated elevated SDHB protein levels in UPS and LMS relative to dedifferentiated LPS. Despite overexpression of SDH subunits, metabolomic profiling demonstrated a significantly higher succinate-to-fumarate ratio in UPS, suggesting functional impairment of SDH enzymatic activity potentially due to posttranslational modifications, altered assembly of SDH subunits, or imbalanced tricarboxylic acid flux. This paradoxical phenotype of SDH overexpression with enzymatic dysfunction defines a unique molecular and metabolic subtype of UPS with prognostic significance. Recognition of this distinct SDH-associated molecular and metabolic phenotype provides insights into UPS pathogenesis, identifies a potential novel prognostic biomarker, and suggests a new avenue for metabolic-targeted therapy. Significance: This study identified a paradoxical phenotype of SDH subunit overexpression with functional impairment in UPS, defining a molecular/metabolic subtype associated with poor prognosis. It offers new data on UPS pathogenesis and treatment.

Supplementary Figure 25 from Succinate Dehydrogenase B (SDHB) Overexpression with Enzymatic Dysfunction Defines a Distinct Subtype of Undifferentiated Pleomorphic Sarcoma

Supplementary Figure 3 from Succinate Dehydrogenase B (SDHB) Overexpression with Enzymatic Dysfunction Defines a Distinct Subtype of Undifferentiated Pleomorphic Sarcoma

SDHB IHC in sarcomas: Differences in immunostaining intensity related to tumoral heterogeneity and cell morphology. Spindle cells with scarce and ill-defined cytoplasm tend to show a more focal and weak staining (A); epithelioid and pleomorphic cells, as well as multinucleated giant cells, with a more voluminous cytoplasm tend to show more granularity and diffusely intense staining (B and C).