Abstract LB-075: CDK12-mutated lethal prostate cancers: How hot are these tumors
Authors: Gurel Bora , Rescigno Pasquale , Yuan Wei , Pereira Rita , Crespo Mateus , Rediti Mattia , Figueiredo Ines , Barrero Maialen , Bianchini Diletta , Fenor de la Maza Maria D. , Chandran Khobe , Carmichael Juliet , Paschalis Alec , Sharp Adam , Seed George , Riisnaes Ruth , Bertan Claudia , Carreira Suzanne , De Bono Johann S. 
Published: September 2020

Abstract
Background: Genomic analyses describing the molecular landscape of primary prostate cancer (PCa) and metastatic castration-resistant prostate cancer (mCRPC) have identified recurrent CDK12 alterations in 2-4% of primary PCa and 4-11% of mCRPC. These aberrations, as well as high lymphocyte tumor infiltration, could be clinically relevant as putative biomarkers of response to immunotherapies. However, there are few studies looking into whether CDK12 biallelic mutant cases are immune ‘hot'. Here, we describe a cohort of patients with CDK12 aberration and studied the tumor infiltration of those cancers.
Methods: Patients with mCRPC and available diagnostic archival and/or CRPC tumor samples were evaluated. Mutation analysis involved custom designed targeted sequencing on MiSeq sequencer. Loss of heterozygosity (LOH) was assessed for the CDK12 cases from exome sequencing using ASCAT, which include single copy lost or copy neutral LOH. Tumor infiltrating lymphocytes were assessed initially with CD3 IHC, using a deep learning-based AI analysis approach. We then subtyped the TILs using a multiplex IF approach, classifying lymphocytes using CD4, CD8 and FOXP3 positivity.
Results: Overall 913 samples (between Feb/15 and Oct/19) were sequenced by targeted NGS, 42 patients presented with pathogenic alterations in CDK12 (4.6%), 27 had bi-allelic alterations, 14 mono-allelic, 1 likely biallelic. In these cases, we identified 39 frameshift alterations, 10 missense mutations mainly involving the kinase domain; with 5 having concomitant LOH. One case showed deep deletion of CDK12 and five presented with additional aberrations in other DNA repair related genes. CDK12 biallelic alterations were present in all 3 cases with both diagnostic and matched mCRPC samples available. We studied T cell infiltration in 100 (23 CDK12 biallelic alterations, 7 monoallelic, 70 controls) samples selected from within the initial targeted NGS cohort. Median intratumoral CD3+ cell density was significantly higher in CDK12 biallelic loss samples compared to matched controls in diagnostic biopsies (271.4 vs 104.683 cells/mm2, p=0.026). A similar trend was seen in mCRPC samples (142.130 vs 51.75 cells/mm2, p=0.36). Intratumoral CD4+ cell infiltration was again significantly higher in CDK12 biallelic loss samples compared to controls (98.864 vs 6.188 cells/mm2, p=0.014).
Conclusions: In our analysis we show that a proportion of mCRPC patients harbor defects in CDK12, these are often alterations involving both alleles, likely present from the time of diagnosis. A majority of these CDK12 altered cancers has high CD3 infiltration compared to controls. We envision that these CDK12 aberrant ‘hot' tumors could represent a subset of mCRPC likely to respond to immune-checkpoint inhibition.
Citation Format: Bora Gurel, Pasquale Rescigno, Wei Yuan, Rita Pereira, Mateus Crespo, Mattia Rediti, Ines Figueiredo, Maialen Barrero, Diletta Bianchini, Maria D. Fenor de la Maza, Khobe Chandran, Juliet Carmichael, Alec Paschalis, Adam Sharp, George Seed, Ruth Riisnaes, Claudia Bertan, Suzanne Carreira, Johann S. De Bono. CDK12-mutated lethal prostate cancers: How hot are these tumors [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 LB-075.