PROTAC-Based Protein Degradation as a Promising Strategy for Targeted Therapy in Sarcomas

Abstract

Sarcomas are heterogeneous bone and soft tissue cancers representing the second most common tumor type in children and adolescents. Histology and genetic profiling discovered more than 100 subtypes, which are characterized by peculiar molecular vulnerabilities. However, limited therapeutic options exist beyond standard therapy and clinical benefits from targeted therapies were observed only in a minority of patients with sarcomas. The rarity of these tumors, paucity of actionable mutations, and limitations in the chemical composition of current targeted therapies hindered the use of these approaches in sarcomas. Targeted protein degradation (TPD) is an innovative pharmacological modality to directly alter protein abundance with promising clinical potential in cancer, even for undruggable proteins. TPD is based on the use of small molecules called degraders or proteolysis-targeting chimeras (PROTACs), which trigger ubiquitin-dependent degradation of protein of interest. In this review, we will discuss major features of PROTAC and PROTAC-derived genetic systems for target validation and cancer treatment and focus on the potential of these approaches to overcome major issues connected to targeted therapies in sarcomas, including drug resistance, target specificity, and undruggable targets. A deeper understanding of these strategies might provide new fuel to drive molecular and personalized medicine to sarcomas.

Keywords: BET proteins; BRD9; PROTAC; SMARCA4; degradation tag; fusion genes; sarcomas; targeted therapy; ubiquitination.

Figure 1

Schematic representation of the mechanisms of action of PROTAC and PROTAC-based genetic tools. The (left panel) depicts a schematic of PROTAC structure and its capability to induce protein target degradation through the recruitment of the cellular ubiquitin–proteasome system. The (right panel) shows the experimental strategy for genetically fusing proteins of interest with a degron tag susceptible to the binding of specific degron PROTACs which induce proteasome-mediated protein degradation.

Figure 2

Schematic representation of targeting strategies for EWS::FLI1 and relative interactors using PROTAC-based protein degradation compared to small molecules inhibitors in EWS. On the (left), EWS::FLI1 acts in complexes also containing ETV6, BRD4, and RHA, while protein degradation of EWS::FLI1 is regulated by TRIM8 E3 ligase and CK1; in the (center), available inhibitors against these mediators include BET inhibitors, which block the BET proteins binding to target genes, and RHA inhibitors, which disrupt the interaction between EWS::FLI1 and RHA; on the (right), PROTAC-based approaches including the dTAG system and PROTAC degraders may deplete EWS::FLI1, TRIM8, ETV6, CK1, and BRD4. Biological responses critical for gene transcription and downstream cell proliferation are reported.

Figure 3

Schematic representation of the functional consequences of BET protein inhibition versus protein degradation in osteosarcoma. (Left): Untreated osteosarcoma cells express high levels of BET proteins BRD2, BRD3, BRD4 (BRD2/3/4), which recognize acetylated histones, thereby activating the transcription of indicated oncogenic target genes. (Center): Treatment with BET inhibitors partially blocks the BET proteins binding to target genes. (Right): BET PROTACs induce protein degradation of BRD2/3/4. Biological responses critical for gene transcription and downstream cell proliferation and apoptosis are reported.

Figure 4

Schematic representation of the functional consequences of SMARCA2/A4 inhibition versus protein degradation in alveolar rhabdomyosarcoma (ARMS). (Left): Untreated ARMS cells express PAX3::FOXO1, which shares proximity on chromatin with SMARCA4, the catalytic ATPase subunit of the SWI/SNF complexes. (Center): Treatment with SMARCA2/4 inhibitor blocks the binding to DNA. (Right): Specific PROTAC induces protein degradation of SMARCA2/4. Biological responses critical for chromatin occupancy, gene transcription, and downstream cell proliferation and differentiation are reported.

Figure 5

Schematic representation of the functional consequences of BRD9 inhibition versus protein degradation in synovial sarcoma. (Left): Untreated synovial sarcoma cells express SS18::SSX which integrates into the BAF complex along with BRD9. (Center): Treatment with BRD9 inhibitors partially blocks the chromatin occupancy of this complex to the DNA. (Right): BRD9 PROTAC induces protein degradation of BRD9. Biological responses critical for chromatin occupancy, gene transcription, and downstream cell proliferation and are reported.