(P 401) OVEREXPRESSION OF CYCLIN DEPENDENT KINASES AND CYCLINS ACROSS SARCOMAS BEYOND CDK4

Objective: Derangements in CDK4 and subsequent effects on the cell cycle have been described across sarcomas—most notably in liposarcoma (LPS), where the use of CDK4/6 inhibitors has been encouraging. However, other CDKs and their paired cyclins have important roles across malignancies. Consequently, inhibitors of CDK7, CDK9, and more are in development. We aimed to identify overexpressers of CDKs/cyclins across bone and soft tissue sarcomas in order to direct future investigation into their clinical relevance and novel therapeutic targeting.

Methods: DNA (592-gene or whole exome; N=7028) and RNA (whole transcriptome; N=3757) sequencing of 45 known genes encoding CDKs and cyclins was performed from sarcoma patient samples, representing 49 subtypes, submitted to Caris Life Sciences (Phoenix, AZ). High RNA expression of CDK/cyclin genes was defined as ≥ 1 and 2 standard deviations (SD) above the overall mean expression of each gene across all subtypes. We then identified the proportion of samples within each subtype that expressed CDK/cyclin genes ≥ 2 SD above the means, and we considered a threshold of ≥ 25% of samples significant for future evaluation. Samples were then evaluated for coincident expression of genes if the subtype-specific groups were found to overexpress multiple assessed genes.

Results: Multiple subtypes were found to have ≥ 25% of cases exhibiting overexpression of CDK/cyclin genes ≥ 2 SD above the grouped means per gene, as judged by RNA transcripts per million. Expected findings included CDK4 RNA overexpression by 145/224 (66%) cases of dedifferentiated LPS, 14/36 (39%) of well differentiated LPS, and 29/75 (39%) of LPS not otherwise specified. These correlated with amplifications of CDK4 in 65-86% of cases. Also expected was CCND1 overexpression in 28/97 (29%) cases of Ewing sarcoma, consistent with prior descriptions. Within rhabdomyosarcomas (RMS), 8/31 cases (26%) of alveolar RMS overexpressed CCND2, and 9/31 (29%) overexpressed CCNE1; 2 cases overexpressed both. 3/10 (30%) cases of spindle cell RMS overexpressed each of CDK6 and CDK8 (1 coincident), and 6/19 (32%) of embryonal RMS overexpressed CDK8. Chordoma was found to overexpress CDK7 in 33/78 (42%) of cases and CDK18 in 29/78 (37%) of cases; the majority of these (20) were coincident overexpressers. Clear cell sarcoma (CCS) overexpressed CDK2 (12/27, 44%) and CCNA1 (10/27, 37%); coincident overexpression was seen in 4 cases. Additionally, 10/37 (27%) of round cell sarcomas (RCS) overexpressed CCND2. Finally, 3/12 (25%) of intimal sarcomas overexpressed CDK4, 7/26 (27%) of epithelioid sarcomas overexpressed CCNA1, and 4/14 (29%) of PNETs overexpressed CCNB3. Although there were associations with a small number of other subtypes, there were fewer than 10 instances of each in the database, making interpretation difficult.

Conclusion: We identified overexpressers of CDK and cyclin genes among a heterogeneous sample of sarcoma patients. By setting a threshold of 2 SD above the mean of each gene we captured the top ~2% of expressers, and by considering subtypes with ≥ 25% of cases above that threshold we accurately identified known associations between CDK4/LPS and CCND1/Ewing sarcoma while also revealing new associations. The most notable overexpressers were chordoma (CDK7, CDK18), CCS (CDK2, CCNA1), RCS (CCND2), and RMS (CDK6, CDK8, CCND2, CCNE1). Associations between high expressers, other relevant mutations/fusions, and transcriptional signatures are under way. These mostly novel findings may be especially relevant in diseases where there no standard accepted therapies exist (e.g. chordoma, CCS). Future investigations may focus on the prognostic and predictive implications of these biomarkers (especially at different transcriptional thresholds), whether they drive tumorigenesis, and if relevant therapeutic targeting yields clinical benefit.