Genomic Profiling of Highly Aggressive Musculoskeletal Sarcomas Identifies Potential Therapeutic Targets: A Single-Center Experience
by
, , , , , , , , , , , , and
Alessandro Parra
1, 
Emanuela Palmerini
2
,
Maria Antonella Laginestra
3,
Cristina Ferrari
3,
Stefania Cocchi
1,
Elisa Simonetti
3,
Evelin Pellegrini
3,
Alessandra De Feo
3,
Giovanna Magagnoli
1,
Giorgio Frega
2,
Davide Maria Donati
4,
Marco Gambarotti
1,
Toni Ibrahim
2
,
Katia Scotlandi
3
,
Lorena Landuzzi
3,* and
Laura Pazzaglia
3 1
Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
2
Osteoncology, Bone and Soft Tissue Sarcomas, and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
3
Laboratory of Oncology Research and Functional Genomics, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
4
Clinica Ortopedica e Traumatologica III a Prevalente Indirizzo Oncologico, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
*
Author to whom correspondence should be addressed.
Cancers 2026, 18(1), 139; https://doi.org/10.3390/cancers18010139
Submission received: 19 November 2025
/
Revised: 22 December 2025
/
Accepted: 29 December 2025
/
Published: 31 December 2025
(This article belongs to the Special Issue Overcoming Chemoresistance in Cancer: Identifying Biomarkers and Novel Targets)
Simple Summary
The clinical heterogeneity of sarcomas, together with the complexity of their genomic landscape, has severely limited novel therapeutic opportunities. We report on our experience at the IRCCS Istituto Ortopedico Rizzoli using targeted gene sequencing for genome profiling with the intent of identifying potential actionable targets. We analyzed 22 advanced sarcoma patients. Genetic alterations in the NOTCH4, AR, BARD1, MUC16, and ROS1 genes, including missense, deletion, duplication, and delins, were the most frequent. Copy Number alterations affected the CDKN2A, CDKN2B, TP53, RHOA, MYC, CCND3, DDR2 genes. In four patients, longitudinal analysis of subsequent lesions highlighted an increase in mutations, like missense or splice variants in the PMS2, SMARCA4, ARID1A, AKT1, BMPR1A, and PTEN genes, suggesting tumor evolution. Our experience, aimed at refining clinical tumor profiling to identify potential therapies, highlighted the issue of the complexity introduced by mutational oncology and the primary role of the Molecular Tumor Board in the clinical management of advanced sarcoma patients.
Abstract
Background/Objectives: Targeted gene sequencing (TGS) for Comprehensive Genomic Profiling (CGP) use in sarcomas has recently increased in clinical practice. We report on TGS real-world data over a period of 3 years (2022–2025) at the IRCCS Istituto Ortopedico Rizzoli, with the aim of identifying potential actionable targets and providing therapeutic indications for advanced sarcoma patients. Methods: We analyzed 22 advanced sarcoma patients by using the VariantPlex Pan Solid Tumor kit panel, including 185 genes. In nine cases, saliva samples for germinal DNA analysis were available. Sequencing was performed on the NextSeq-500 Platform and analyzed with Archer Analysis software. The Cancer Genome Interpreter and OncoKB Database tools were used to find potential actionable targets. Results: We found the most frequent genetic variants, including missense, deletion, duplication, and delins, in the NOTCH4, AR, BARD1, MUC16, and ROS1 genes. Copy Number alterations affected the CDKN2A, CDKN2B, TP53, RHOA, MYC, CCND3, and DDR2 genes mainly in osteosarcoma samples. In four patients, longitudinal analyses of subsequent lesions showed the maintenance of most genomic alterations and enrichment in missense or splice variants in PMS2, SMARCA4, ARID1A, AKT1, BMPR1A, and PTEN, indicating the occurrence of tumor evolution. Germline variants subtraction identified the specific somatic tumor mutations. Advantages and disadvantages of our approach were considered in order to refine the analysis setting and better select possible actionable targets. Conclusions: Early access to genomic analyses, routine germline assessment, and broad gene panels would help in identifying possible targeted drugs with sufficient evidence of activity beneficial to each patient. In the clinical management of advanced sarcoma patients, when analyzing cost-effectiveness and sustainability, the role of the Molecular Tumor Board in the governance of the complexity introduced by mutational oncology should be considered.
