Frank Sander, Persse Thomas, Coleman Ilsa, Bankhead Armand, Li Dapei, De-Sarkar Navonil, Wilson Divin, Rudoy Dmytro, Vashisth Manasvita, Galipeau Patty, Yang Michael, Hanratty Brian, Dumpit Ruth, Morrissey Colm, Corey Eva, Montgomery R Bruce, Haffner Michael C, Pritchard Colin, Vasioukhin Valera, Ha Gavin, Nelson Peter S
Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119.
Divison of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98119.
bioRxiv. 2024 Jul 19:2024.07.16.603734. doi: 10.1101/2024.07.16.603734.
Genomic loss of the transcriptional kinase occurs in ~6% of metastatic castration-resistant prostate cancers (mCRPC) and correlates with poor patient outcomes. Prior studies demonstrate that acute CDK12 loss confers a homologous recombination (HR) deficiency (HRd) phenotype via premature intronic polyadenylation (IPA) of key HR pathway genes, including However, mCRPC patients have not demonstrated benefit from therapies that exploit HRd such as inhibitors of polyADP ribose polymerase (PARP). Based on this discordance, we sought to test the hypothesis that an HRd phenotype is primarily a consequence of acute loss and the effect is greatly diminished in prostate cancers adapted to loss. Analyses of whole genome sequences (WGS) and RNA sequences (RNAseq) of human mCRPCs determined that tumors with biallelic alterations ( ) lack genomic scar signatures indicative of HRd, despite carrying bi-allelic loss and the appearance of the hallmark tandem-duplicator phenotype (TDP). Experiments confirmed that acute CDK12 inhibition resulted in aberrant polyadenylation and downregulation of long genes (including and ) but such effects were modest or absent in tumors adapted to chronic . One key exception was , which did retain transcript shortening and reduced protein expression in the adapted models. However, cells demonstrated intact HR as measured by RAD51 foci formation following irradiation. cells showed a vulnerability to targeting of CDK13 by sgRNA or CDK12/13 inhibitors and treatment of prostate cancer xenograft lines showed that tumors with responded to the CDK12/13 inhibitor SR4835, while CDK12-intact lines did not. Collectively, these studies show that aberrant polyadenylation and long HR gene downregulation is primarily a consequence of acute CDK12 deficiency, which is largely compensated for in cells that have adapted to CDK12 loss. These results provide an explanation for why PARPi monotherapy has thus far failed to consistently benefit patients with CDK12 alterations, though alternate therapies that target CDK13 or transcription are candidates for future research and testing.
转录激酶的基因组缺失发生在约6%的转移性去势抵抗性前列腺癌（mCRPC）中，并且与患者的不良预后相关。先前的研究表明，急性CDK12缺失通过关键同源重组（HR）途径基因（包括……）的过早内含子聚腺苷酸化（IPA）赋予同源重组缺陷（HRd）表型。然而，mCRPC患者尚未从利用HRd的疗法（如聚ADP核糖聚合酶（PARP）抑制剂）中获益。基于这种不一致性，我们试图检验以下假设：HRd表型主要是急性……缺失的结果，而在适应了……缺失的前列腺癌中这种效应会大大减弱。对人类mCRPC的全基因组序列（WGS）和RNA序列（RNAseq）的分析确定，具有双等位基因……改变（……）的肿瘤缺乏指示HRd的基因组疤痕特征，尽管携带双等位基因缺失并出现标志性的串联复制子表型（TDP）。实验证实，急性CDK12抑制导致长基因（包括……和……）的异常聚腺苷酸化和下调，但在适应慢性……的肿瘤中这种效应较小或不存在。一个关键的例外是……，其在适应……的模型中确实保留了转录本缩短和蛋白质表达降低的情况。然而，……细胞在照射后通过RAD51灶形成测量显示出完整的HR。……细胞显示出对sgRNA或CDK12/13抑制剂靶向CDK13的敏感性，并且对前列腺癌异种移植瘤系的……治疗表明，具有……的肿瘤对CDK12/13抑制剂SR~4835有反应，而CDK12完整的瘤系则没有。总体而言，这些研究表明，异常聚腺苷酸化和长HR基因下调主要是急性CDK12缺陷的结果，而在适应了CDK12缺失的细胞中这种情况在很大程度上得到了补偿。这些结果解释了为什么PARPi单药治疗迄今未能持续使携带CDK12改变的患者获益，尽管靶向CDK13或转录的替代疗法是未来研究和测试中的候选方案。
