ECP 2023 Abstracts

S46 Virchows Archiv (2023) 483 (Suppl 1):S1–S391 13 rarity. Our aim was to characterise key events in osteosarcoma using multiregional whole genome sequencing. Methods: We uniformly processed 185 osteosarcoma whole genomes from 41 patients generated via two sequencing projects (100,000 Genome Project and Gabriella Miller Kids First Paediatric Data Resource). Intratumoral diversity was characterised based on driver alterations, mutational signatures, and complex rearrangements including chromothripsis. Phylogenetic and timing analyses were then employed to determine the order of these genomic features in osteo- sarcoma development. Results: Our analyses reveal commonly reported drivers in osteosar- coma are frequently subclonal (NF1-58%, PTEN- 60%, ATRX- 72%). In addition, while chromothripsis and complex genomic rearrange- ments (CGRs) are typically clonal, a significant number of subclonal structural alterations make up these CGRs, adding to regional diversity. Whole genome duplication (WGD) are late events in these tumours, and CGRs are found to occur mainly after WGD, providing evidence for their role as driver-like events triggering clonal diversification. Finally applying timing approaches to determine the order of struc- tural alterations within these complex rearrangements reveals foldback inversions as an important initiator of amplifications in osteosarcoma. Conclusion: Our work highlights the extent of genetic subclonal diver- sity in osteosarcoma. Here we also demonstrate that CGRs are not static events but continue to evolve throughout a tumour lifespan, priming the genome for further instability. These findings have important implica- tions for therapeutic approaches to osteosarcoma and other genomically unstable cancers. Through timing of complex structural events, we reveal common initiating mechanisms of driver events, furthering our understanding of osteosarcoma development. OFP-12-003 Calcified chondroid mesenchymal neoplasms: expanding the molecular and morphological spectrum C. Bouvier*, C. Benard, F. Le Loarer, R. Azmani, J. Garcia, I. Hostein, M. Karanian, A. Meurgey, F. Tirode, N. Macagno *Hôpital de la Timone, France Background & objectives: Soft tissue tumours with chondroid matrix and calcifications are frequently found at the extremities or the tem- poromandibular joint. Recently FN1 fusions to genes encoding RTK (receptor tyrosine kinases) were identified in close mimics: «calcified chondroid mesenchymal neoplasms (CCMT)». Methods: In order to define the morphological spectrum of these tumours we gathered together 41 tumours diagnosed in the french net- work of soft tissue and bone tumours. The final diagnosis was done with morphological and clinicoradiological data. We performed whole RNA sequencing, transcriptomic and methylome profiling. Results: We found 6 synovial chondromatoses, 2 mesenchymal phos- phaturic tumours and 33 CCMT which encompassed 15 soft tissue chondromas (CD), 10 tophaceous pseudogouts (TPG) and 8 chondroid tenosynovial giant cell tumours (TCGT). 28/33 had fusions with FN1 gene, with varied partners including FGFR2 (13 cases) and TEK (8 cases). All the FN1::TEK-fused tumours were located in the tempo- romandibular joint and had morphological features of TCGT. They formed a distinct subgroup on unsupervised trancriptomic and methyl- ome clustering analyses. CD and TPG were located in a distinct molec- ular subgroup aside from other chondroid neoplasms such as synovial chondromatosis and acral fibrochondromyxoid tumours. Conclusion: FN1-fused CCMT share several morphological fea- tures that overlap with CD, TPG and TCGT. Interestingly some TCGT located in the temporomandibular joint were devoid of chondroid matrix and harboured a FN1::TEK fusion expanding the molecular spectrum of TCGT. Surgical resection is the rule but in cases of recurrence or bone erosion tyrosine kinase inhibitors could be an alternative treatment. OFP-12-004 Unravelling homologous recombination repair deficiency and ther- apeutic opportunities in soft tissue and bone sarcoma C. Pauli*, L. Planas-Paz, A. Pliego Mendieta *USZ and UZH, Switzerland Background & objectives: Homologous Recombination Deficiency (HRDness) has become of major clinical relevancein cancer therapy but remains poorly investigated in sarcoma. We here broaden the under- standing of HRDness in soft tissue and bone sarcoma by performing a comprehensive molecular and functional analysis. Methods: We investigated genomic and transcriptomic features of HRDness in sarcoma and cross-validated our findings from different sarcoma subtypes among several datasets. We established patient- derived ex vivo sarcoma cell models and functionally tested the sensi- tivity of our models to several targeted therapies including PARPi as gold standard treatment for HRDness and chemotherapies in mono- therapy or in combination. Results: We show that specific sarcoma entities exhibit high levels of genomic instability signatures and molecular alterations in HRR genes, while harbouring a complex pattern of chromosomal instabil- ity. Furthermore, sarcomas carrying HRDness traits exhibit a distinct SARC-HRD transcriptional signature that predicts PARPi sensitivity in patient-derived sarcoma cell models. Concomitantly, HRDhigh sar- coma cells lack RAD51 nuclear foci formation upon DNA damage, further evidencing defects in HRR. We further identify the WEE1 kinase as a therapeutic vulnerability for sarcomas with HRDness and demonstrate the clinical benefit of combining DNA damaging agents and inhibitors of DNA repair pathways ex vivo and in the clinic. Conclusion: HRDness in tumours correlate with poor prognosis and has become of major clinical relevance as it is associated with thera- peutic vulnerabilities and remains poorly investigated in sarcoma. We show that a subset of sarcoma entities exhibit features of HRDness at the genomic and transcriptomic level and highlight the need to charac- terize sarcoma patients with multiple parameters to better identify those with HRDness. In summary, we provide a personalized oncological approach to treat sarcoma patients successfully. Funding: Swiss Cancer League KFS 5270-03-2021 OFP-12-005 Recurrent USP6 rearrangement in a subset of low grade myofibro- blastic sarcomas of the soft tissues G. Arcovito*, S. Crucitta, M. Del Re, C. Caporalini, A. Palomba, F. Nozzoli, A. Franchi *University of Pisa, Italy Background & objectives: USP6 gene rearrangement typically occurs in benign entities like nodular fasciitis. Nevertheless, rare cases of USP6-rearranged myofibroblastic neoplasms with locally aggressive behaviour have been described. The role of USP6 in low grade myofi- broblastic sarcomas (LGMSs) has not yet been investigated. Methods: On the basis of 2 index cases of LGMS which presented USP6 rearrangement by RNA sequencing (Archer FusionPlex panel), we extended our analysis to a series of 10 cases of low-grade sarcoma with similar morphology and immunohistochemical features, perform- ing fluorescent in situ hybridization (FISH) analysis with USP6 break- apart probe. All the available histological and immunohistochemical slides were reviewed. Results: In the 2 index cases, RNA sequencing identified USP6::THBS2 and USP6::RRBP1 fusions, and rearrangement of USP6 was confirmed by FISH. One further case presented USP6 rearrangement by FISH. Six tumours showed no rearrangement of USP6, while in 3 cases results were not evaluated due to poor DNA quality. USP6-rearranged tumours arose in deep soft tissues of the extremities in adults. Histologically, they presented