Characterizing CDK12-Mutated Prostate Cancers

Abstract

Purpose: Cyclin-dependent kinase 12 (CDK12) aberrations have been reported as a biomarker of response to immunotherapy for metastatic castration-resistant prostate cancer (mCRPC). Herein, we characterize CDK12-mutated mCRPC, presenting clinical, genomic, and tumor-infiltrating lymphocyte (TIL) data.

Experimental design: Patients with mCRPC consented to the molecular analyses of diagnostic and mCRPC biopsies. Genomic analyses involved targeted next-generation (MiSeq; Illumina) and exome sequencing (NovaSeq; Illumina). TILs were assessed by validated immunocytochemistry coupled with deep learning-based artificial intelligence analyses including multiplex immunofluorescence assays for CD4, CD8, and FOXP3 evaluating TIL subsets. The control group comprised a randomly selected mCRPC cohort with sequencing and clinical data available.

Results: Biopsies from 913 patients underwent targeted sequencing between February 2015 and October 2019. Forty-three patients (4.7%) had tumors with CDK12 alterations. CDK12-altered cancers had distinctive features, with some revealing high chromosomal break numbers in exome sequencing. Biallelic CDK12-aberrant mCRPCs had shorter overall survival from diagnosis than controls [5.1 years (95% confidence interval (CI), 4.0-7.9) vs. 6.4 years (95% CI, 5.7-7.8); hazard ratio (HR), 1.65 (95% CI, 1.07-2.53); P = 0.02]. Median intratumoral CD3⁺ cell density was higher in CDK12 cancers, although this was not statistically significant (203.7 vs. 86.7 cells/mm²; P = 0.07). This infiltrate primarily comprised of CD4⁺FOXP3^- cells (50.5 vs. 6.2 cells/mm²; P < 0.0001), where high counts tended to be associated with worse survival from diagnosis (HR, 1.64; 95% CI, 0.95-2.84; P = 0.077) in the overall population.

Conclusions: CDK12-altered mCRPCs have worse prognosis, with these tumors surprisingly being primarily enriched for CD4⁺FOXP3^- cells that seem to associate with worse outcome and may be immunosuppressive.See related commentary by Lotan and Antonarakis, p. 380.

Figure 1.

A. Lollipop plot depicting mutations in CDK12 in this prostate cancer cohort with biallelic alterations (n=31); missense mutations are depicted in green, frameshift and non-sense mutations in black. B. OncoPrint figure representing CDK12 mutations for the bi-allelic tumors in hormone sensitive prostate cancer (HSPC) and metastatic castration-resistant (mCRPC) samples (top figures). Middle panel shows concomitant alterations in other DNA repair genes and other relevant pathways in prostate cancer, detected on targeted and exome sequencing in diagnostic and/or mCRPC samples. Bottom panel depicts the available immunohistochemistry (IHC) data for PTEN and ATM on the samples sequenced. PTEN and ATM data were respectively available for 16 and 17 samples of the 31 CDK12 biallelic cases. Grey boxes indicate sample with no available PTEN or ATM results by IHC,

Figure 2.

Survival curves: A. Kaplan-Meier curves for overall survival from date of diagnosis. CDK12 biallelic mutation cases in yellow, controls in blue. B. Kaplan-Meier curves for overall survival from date of diagnosis. CDK12 biallelic and monoallelic mutated cases in yellow, controls in blue. C. Kaplan-Meier curves for overall survival from date of castration resistant prostate cancer (CRPC) diagnosis. CDK12 biallelic mutated cases in yellow, controls in blue. D. Kaplan-Meier curves for overall survival from date of castration resistant prostate cancer (CRPC) diagnosis. CDK12 biallelic and monoallelic mutated cases in yellow, controls in blue.

Figure 3.

Genomic analyses: A. Copy number breaks (CNBs) determined from exome sequencing data in n=211 patients. CDK12 biallelic mutation cases (n=23) in red, monoallelic cases (n=3) in yellow, and cancers with no CDK12 alterations (controls) in blue. The black line indicates the median number of CNBs (median =513) in the whole cohort. B. Violin plot depicting CNB numbers in CDK12 mutated in red and controls in blue.

Figure 4.

Tumor infiltrating lymphocytes (TILs) analyses: A. Intratumoral CD3⁺ TILs per mm². Bar Chart depicting intratumoral CD3+/mm² density (y-axis) in CDK12 biallelic cases in red, monoallelic cases in yellow, and controls in blue. B. Box and Whisker plot of log10-transformed intratumoral CD3+ cell density per mm² depicting CDK12 biallelic in red, monoallelic cases in yellow, and control cases in blue.

Figure 5.

Tumor infiltrating lymphocyte (TIL) subset analyses: A. i) Scatter plots depicting associations between log-transformed CD3⁺ cells/mm² TILs and CD4⁺FOXP3⁻ cells/mm², ii) CD3⁺ cells/mm² and CD8⁺cells/mm², as well as iii) CD3⁺ cells/mm² and CD4⁺FOXP3+cells/mm². B. Box and whisker plots representing intratumoral infiltrate density as log10-transformed CD4⁺FOXP3⁻ cells/mm² (i), CD8⁺cells/mm² (ii), CD4⁺ FOXP3⁺cells/mm² (iii) in CDK12 biallelic (red), monoallelic (yellow), and control cases (blue); iv) Tumor CD4⁺FOXP3⁻/CD8⁺ ratio between biallelic cases (red) and controls (blue).