Fusion-Associated Neoantigen Burden And Predicted Immunogenicity Of Cdk12 Biallelic Loss-Of-Function Tumors Vary Substantially Across Cancer Types

Abstract Background: Biallelic inactivation of CDK12 is associated with a distinct genomic signature of focal tandem duplications (FTDs). Gene fusions resulting from CDK12-associated FTDs increase neoantigen load, raising interest in CDK12 as a biomarker of response to immune checkpoint inhibitors (ICIs). Although FTDs have been detected at higher rates in CDK12-altered tumors compared to CDK12 WT tumors for multiple cancer types, fusion-associated neoantigen burden has only been evaluated in metastatic castration-resistant prostate cancer. Methods: By retrospective review of molecular profiles, we identified tumors with CDK12 biallelic loss-of-function (LOF) in a primary cohort of over 9000 patient tumors, representing 39 cancer types, and assessed fusions detected by whole transcriptome sequencing for immune epitopes. Biomarker and fusion results for a second cohort of over 13,000 patient tumors were reviewed for validation of the initial findings. Results: Tumors with CDK12 biallelic LOF (bLOF) (n=29) had significantly higher mean fusion rates (11.7 fusions/tumor) than CDK12 monoallelic LOF (mLOF) and WT tumors (4.1 and 2.6, respectively). Analysis of fusion topologies and breakpoints indicated a predominance of duplication events for CDK12 bLOF tumors and a bimodal distribution of breakpoint distances (modes at ~250-500 kb and ~1.0-2.5 Mb), consistent with prior reports. Fusion rates correlated with the rate of predicted neoantigens with high, intermediate, and low affinity for MHC class I. Fusion-associated neoantigen burden was significantly higher in CDK12 bLOF tumors (145.0 high affinity peptides/tumor) than mLOF (49.7) and WT (26.6) tumors. Among CDK12-altered tumors, fusion rates were significantly higher in prostate (16.4 fusions/tumor, n=11) and ovarian (19.7, n=6) than other cancer types (3.4 overall, n=12), potentially reflecting cancer type-specific roles for CDK12. Co-occurrence of mismatch repair deficiency (dMMR)/high microsatellite instability (MSI-High) with CDK12 bLOF (n=5), most often in colorectal tumors (n=4), correlated with a lower fusion rate (0.2 fusions/tumor); recurrent CDK12 frameshift mutations in these cases (G1461fs, T1463fs, and Q1291fs) coincide with poly-nucleotide tracts, suggesting CDK12 mutations are a secondary effect. In a separate cohort of over 13,000 patient tumors, additional CDK12 bLOF tumors (n=47) were identified, showing a similar distribution and association with high fusion rate (11.0 fusions/tumor). Conclusion: Fusion rates and predicted neoantigen load varied significantly between CDK12 biallelic tumors across cancer types, highlighting the value of biomarkers with a quantitative immunogenic/phenotypic readout. We propose that fusion rates are linked to CDK12 alterations and may serve as useful biomarker to enhance our ability to identify responders of ICI therapy. Citation Format: Andrew Elliott, Phillip Stafford, Jian Zhang, Qing Zhang, Jeff Swensen, Daniel Martin, Joanne Xiu, Zoran Gatalica, Daniel Vaena, Elisabeth Heath, W. Michael Korn. Fusion-associated neoantigen burden and predicted immunogenicity of CDK12 biallelic loss-of-function tumors vary substantially across cancer types [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3639.