Data to reproduce analysis in Convergent evolution of extrachromosomal DNA in mCRPC paper

Targeted cancer therapies can prolong the lives of men with metastatic castration resistant prostate cancer (mCRPC). However, these treatments also selectively favor the growth of tumor cells that harbor therapy resistance, and mCRPC is currently lethal. It has been challenging to study factors influencing how therapy resistance develops in this setting because few autopsy studies of have been performed in the settings of DNA-repair deficient mCRPC. Here, we assessed how resistance to targeted cancer therapies evolved in an autopsy cohort of 53 mCRPC tumors from six such men using deep whole genome and transcriptome analysis, validating our observations in an independent cohort of 135 mCRPC tumors. We identified intra-patient heterogeneity in clinically actionable DNA repair deficiencies and transcriptionally-defined tumor subtypes. Identical polygenic DNA repair resistance mutations were present in physically distinct tumors within the same individual, suggesting that these mutations pre-exist selection by later targeted therapy. Extra-chromosomal DNA (ecDNA) was present in more than half of mCRPC biopsies and frequently amplified the androgen receptor (<em>AR</em>) and enhancers of <em>AR</em> and <em>MYC</em>. Individual ecDNA amplicons included multiple driver genes on different chromosomes, and arose multiple times within distinct tumors in a single patient. The presence of ecDNA was significantly associated with whole genome doubling, chromothripsis, and with inactivating <em>TP53</em> alterations. We conclude that ecDNA amplification is a major contributor to therapy resistance in mCRPC and that late-stage mCRPC develops intra-patient heterogeneity in response to targeted therapy.靶向癌症疗法可延长转移性去势抵抗性前列腺癌（metastatic castration resistant prostate cancer, mCRPC）男性患者的生存期。然而此类治疗也会选择性地促进携带治疗抗性的肿瘤细胞增殖，且目前mCRPC仍为致死性疾病。由于针对DNA修复缺陷型mCRPC的尸检研究较为匮乏，在此背景下探究治疗抗性产生的影响因素一直颇具挑战。本研究通过深度全基因组及转录组分析，对6名mCRPC患者的53份尸检肿瘤样本开展靶向癌症治疗抗性演化特征分析，并在135份独立mCRPC肿瘤样本队列中验证了本研究的观测结果。研究团队发现，临床可干预的DNA修复缺陷及转录组定义的肿瘤亚型存在患者内异质性。同一患者体内不同解剖部位的肿瘤可携带完全相同的多基因DNA修复抗性突变，提示此类突变在后续靶向治疗的选择压力出现前即已存在。染色体外DNA（extrachromosomal DNA, ecDNA）在超过半数的mCRPC活检样本中存在，且常发生雄激素受体（androgen receptor, AR）及AR、MYC增强子的扩增。单个ecDNA扩增区域可包含不同染色体上的多个驱动基因，且可在同一患者的不同肿瘤中独立多次产生。ecDNA的存在与全基因组倍增、染色体碎裂（chromothripsis）以及TP53基因失活突变显著相关。本研究结论认为，ecDNA扩增是mCRPC治疗抗性的主要驱动因素，且晚期mCRPC会在靶向治疗的压力下产生患者内异质性。